title: GSCLC_2

description:
GSCLC_2.mcool
GSCLC.10kb.fanc
GSCLC.compscore.bw
GSCLC_TAD.bed

data_processing:
Sequences were first trimmed using fastp v0.21.0 with default options and the --detect_adapter_for_pe flag.
Trimmed sequences were then processed using HiCUP v0.8.0 with default options and di-tag length range set to 0-800, with bowtie v2.4.2 as the aligner.
hicup2juicer was then used to produce di-tag files subsequently ingested with Juicer tools v1.22.01 for the creation of .hic files.
The same set of di-tag files were also used to create multi-resolution cooler files using cooler v0.8.10 with default options.
Additionally, HiCSR commit b13ac41 was used to de-noise 10kb-resolution contact maps for visualization.
FAN-C v0.9.13 was finally used for the normalization (with default parameters) and subsequent visualization of the enhanced 10kb matrices, including virtual 4C profiles.
Genome_build: mm10
Supplementary_files_format_and_content: mcool files are multi-resolution cooler files containing balance-normalized count matrices
Supplementary_files_format_and_content: bw files are bigwig files of  compartment score generated from cooltools call-compartments and oriented using GC content
Supplementary_files_format_and_content: bed files describe TADs identified using cooltools diamond-insulation at 10kb resolution with a 100kb window size and a prominence cut-off of 0.2
Supplementary_files_format_and_content: fanc files contain count matrices enhanced by HiCSR and stored through FAN-C

extract_protocol:
in situ Hi-C library preparation was performed as described previously (Belaghzal et al., 2017, Rao et al., 2014) with minor modifications. We used the whole harvested cells for mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs and d4c7 mPGCLCs, and FACS-sorted AAG-positive cells for GSCs and GSCLCs. 2.5 x 106 cells were used for one replicate. The cells were fixed by 1% formaldehyde (Sigma) /HBSS and lysed in lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP-40) for 30 min on ice with frequent inversion. The cells were digested by 500 U of DpnII (NEB) overnight at 37°C. Following biotin filling (Thermo Fisher Scientific, 19524-016; NEB, M0210S), proximity ligation (Thermo Fisher Scientific, 15224090) and reverse crosslinking, DNA was purified by ethanol precipitation and sheared to 200-400bp fragments using Covaris E220 sonicator (Covaris) at 4°C (10% Duty Factor, 200 cycles/burst, 175 W Peak Incident Power, 110 s). Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (Thermo Fisher Scientific)
Library preparation was performed using NEB library preparation kit (NEB, E7645S; NEB, E7335S) according to manufacturer’s guidance. The libraries were amplified 8 cycles and DNA fragments between 300-800bp were selected using AMPure XP beads (Corning).


title: wt_female_tdt_neg

status: Public on Jun 15 2022

type: SRA

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

country: USA

institute: Stanford University

description: Sequenced on two lanes (6 total raw files)

library_source: transcriptomic

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded
Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

molecule: polyA RNA

organism: Mus musculus

source_name: Aortic tissue

extract_protocol:
The aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided midway between the aortic valve and the takeoff of the brachiocephalic artery . Aortas were transferred to a separate dish and rinsed in HBSS. Specimens were combined into groups with age and genotype-matched animals as biologic replicates. The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to seperate fluorescent (tdTomato+) SHF lineage-traced cells and lineage negative cells.. Samples were then processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generate from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

tag: fbn1 genotype

value: Control

tag: lineage

value: Non lineage-traced

tag: Sex

value: Female

tag: tissue

value: Aorta


title: 530_S2-RIP_1

city: Memphis

first: Mario

last: Halic

state: Tennessee

address: 262 Danny Thomas Place

department: Structural Biology

institute: St. Jude Children’s Research Hospital

data_processing:
Sequencing reads obtained in the poly(A) RNA sequencing (pA RNA), Pol II ChIP, nascent RNA sequencing (Pol II RIP) and total RNA sequencing experiments were mapped to the S. pombe reference genome (PomBase, release 2018) using splice-aware alignment tool STAR version 2.7.3a (Dobin et al., 2013).  Alignment of RIP-seq and RNA-seq data was performed with STAR default parameters. Unspliced alignments of ChIP-seq data was enforced through parameters ‘--alignIntronMax 1’ and ‘--alignEndsType EndToEnd’. Reads mapping to ribosomal RNA have been removed from further analysis.
Genomic read counts were obtained using a custom script that extended basic htseq-count functionality with ‘--mode intersection-strict’ option. Additionally, for RNA assays pA RNA, Pol II RIP and total RNA, we used the ‘--stranded yes’ option to disambiguate which strand reads originated from. In short, reads mapping uniquely to protein-coding genes and reads that map less than 16 times were counted and normalized by gene length and sequencing depth (TPM, Transcripts Per Million). We chose 16 (dg/dh have in 12-13 copies) as multi-mapping threshold for heterochromatic genes to eliminate low-complexity reads without discarding reads originating from heterochromatic regions. In the read counting, we did not distinguish between individual gene copies but used one representative copy to collect all reads stemming from any one copy.
Assembly: PomBase, release 2018
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: total RNA

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in rich YES medium.

extract_protocol:
50 ml yeast cultures with an OD600 of 1.2 were cross-linked with 1% formaldehyde (Roth) for 15 min at room temperature. The reaction was quenched with 125 mM glycine for 5 min. The frozen pellet was resuspended in 500 µl lysis buffer (250 mM KCl, 1x Triton-X, 0.1% SDS, 0.1% Na-Desoxycholate, 50 mM HEPES pH 7.5, 2 mM EDTA, 2 mM EGTA, 5 mM MgCl2, 0.1% Nonidet P-40, 20% Glycerol) with 1 mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche). Lysis was performed with 0.25-0.5 mm glass beads (Roth) and the BioSpec FastPrep-24 bead beater (MP-Biomedicals), 8 cycles at 6.5 m/s for 30s and 3 min on ice. DNA was sheared by sonication (Bioruptor, Diagenode) 35 times for 30 s with a 30 s break. Cell debris was removed by centrifugation at 13 000 x g for 15 min. The crude lysate was normalized based on the RNA and Protein concentration (Nanodrop, Thermo Scientific) and incubated with 1.2 µg immobilized (Dynabeads Protein A, Thermo Scientific) antibody against Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam) for at least 2 h at 4°C. The resin with immunoprecipitates was washed five times with each 1 ml of lysis buffer and eluted with 150 µl of elution buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 15 min. Cross-linking was reversed at 95°C for 15 min and subsequent RNase A (Thermo Scientific) digest for 30 min followed by Proteinase K (Roche) digest for at least 2 h at 37°C. DNA was recovered by phenol-chloroform-isoamylalcohol (25:24:1, Roth) extraction with subsequent ethanol precipitation.
For sequencing, a ChIP-seq library was made using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB).

tag: strain number

tag: genotype

tag: target molecule

value: RNA-PolII bound RNA

tag: ip antibody


title: 524_S2-RIP_1

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: cap-h2-2_0h_rep3

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description: SAMPLE 7

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 10.7.3

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 100 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp WT Labeling Kit (Agilent).

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown on MGRL, 1.5% gellan gum medium for two weeks.

extract_protocol: Total RNA was extracted from whole roots of zeocin treated plants using PureLink® Plant RNA Reagent (Thermo Fisher Scientific).

treatment_protocol: Two-weeks-old plants were transferred to container containing half strength of MGRL solution without sucrose. After 3 hours acclimation to hydroponic condition, seedlings were transferred to different containers containing half strength of MGRL with 10 μM zeocin. The whole roots were harvested after the treatment with zeocin for 0, 1 hour, 3 hours and subsequently subjected to total RNA extraction and microarray analysis.

tag: genotype/variation

value: whole roots

tag: treatment

value: 0h zeocin treatment


title: cap-h2-2_0h_rep2

description: SAMPLE 6


title: d4c7PGCLC_netcage_2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: nascent RNA

data_processing:
Library strategy: NET-CAGE
Sequences were first trimmed using fastp v0.21.0
Then trimmed reads were aligned using STAR 2.7.6a using default options.
Uniquely-mapped reads were converted to coverage bigWig tracks with G-bias correction using CAGEr v1.32.0 using default options.
Tag clusters were identified using CAGEfightR v1.7.6 with pooledCutoff = 0.1 and mergeDist = 20 for unidirectional clusters as well as balanceThreshold = 0.8 for bidirectional clusters.
These clusters were subsequently filtered to require at least 1 sample demonstrating expression level exceeding 1 TPM. Unidirectional clusters (putative promoters) were removed if they overlapped bidirectional clusters (putative enhancers), and the two region sets were subsequently combined to identify coordinately regulation enhancer-promoter co-transcription across stages. In particular, this Kendall correlation analysis of finding co-transcribed enhancer clusters within 1mb of expressed promoter clusters with TPM as the expression unit.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are coverage tracks generated by CAGEr v1.32.0 using default options.

growth_protocol: The BDF1-2-1 mouse mESCs bearing Blimp1-mVenus and Stella-ECFP (BVSC) transgenes (Ohta et al., 2021) were cultured as described previously (Hayashi et al., 2011). Briefly, mESCs were maintained in N2B27 medium supplemented with PD0325901 (0.4 uM) (Stemgent), CHIR99021 (3 uM) (Bio Vision), and leukemia inhibitory factor (LIF) (1000 U/ml) (Merck Millipore) on a 12-well plate coated with poly-L-ornithine (0.01%) (Sigma) and laminin (10 ng/ml) (BD Bioscience). In this study, all cells were cultured at 37°C under an atmosphere of 5% CO2 in air. Induction of EpiLCs and PGCLCs was performed as described previously (Hayashi et al., 2011) with minor modifications. Briefly, the EpiLCs were induced by plating 8 x 104 mESCs on a well of 12-well plate coated with human plasma fibronectin (16.7 mg/ml) (Merck Millipore) in N2B27 medium containing activin A (20 ng/ml) (Peprotech), bFGF (12 ng/ml) (Invitrogen), and KSR (1%) (Gibco). PGCLCs were induced from d2 EpiLCs (2 days after induction) under a floating condition in wells of a low-cell-binding U-bottom 96-well plate in GMEM medium (Thermo Fisher Scientific) containing 15% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific) and 2mM L-glutamin (Thermo Fisher Scientific) supplemented with BMP4 (500 ng/ml) (RSD), LIF (1000 U/ml) (Merck Millipore), SCF (100 ng/ml) (RSD), EGF (50 ng/ml) (RSD). The expansion culture of PGCLCs was performed as previously described (Ohta et al., 2021). Briefly, following incubation in TrypLE™ Express (Gibco) for 10 min, the aggregates of d4 mPGCLCs (PGCLCs induced for 4 days) were dissociated into single cells by rigorous pipetting. Subsequently, BV-positive cells were sorted with a FACSAriaIII cell sorter. Purified d4 mPGCLCs were cultured on m220-5 cells as the feeder cells in GMEM (Gibco) containing 10% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 2.5% FBS (Hyclone), SCF (100 ng/ml) (RSD), 10 uM forskolin (Sigma), 10 uM rolipram (abcam), 5 uM CsA (Sigma). Half of the culture medium was changed every two days. GSCs and GSCLCs bearing Acro/Act-EGFP (AAG) transgenes (Ishikura et al., 2016) were cultured as described previously (Ishikura et al., 2016). Briefly, cells were cultured in Stempro-34 SFM supplemented with Stempro Supplement (Gibco), with 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 1% FBS (Hyclone), 1xMEM vitamin solution (Thermo Fisher Scientific), 5.0mg/ml AlbMAXI (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 1x Insulin-Transferrin-Selenium (ITS-G) (Gibco), 10 ng/ml bFGF (Invitrogen), 20 ng/ml GDNF Rat Recombinant (RSD), 20 ng/ml EGF (RSD), and 1000 U/ml LIF (Merck Millipore) in a well of 6-well plate on mouse embryonic fibroblast cells (MEFs) as feeder cells. Half of the medium was replaced every two or three days.

extract_protocol:
NET-CAGE library preparation was performed as described previously (Hirabayashi et al., 2019) with minor modifications. For extraction of nascent RNA, cells were firstly lysed with 1400 μl Buffer A, which is Nuclei EZ Lysis Buffer (Sigma) supplemented with 25 μM α-amanitin (Wako), 1× cOmplete Protease Inhibitor Cocktail (Roche, 4693116001) and SUPERase•IN RNase Inhibitor (20 units; Thermo Fisher Scientific), was incubated on ice for 10 min and centrifuged at 800 g for 5 min at 4°C followed by wash once with the same buffer. Washed pellets were resuspended in 200μl Buffer B, containing 1% NP-40, 20 mM HEPES pH7.5, 300 mM NaCl, 2 M urea, 0.2 mM EDTA, 1 mM dithiothreitol (DTT) (Promega), 25 μM α-amanitin, 1× cOmplete Protease Inhibitor Cocktail and SUPERase•IN RNase Inhibitor (20 units), and incubated for 10 min on ice. The suspension was centrifuged at 3000g for 2 min at 4°C. After removing the supernatant, the nuclear insoluble fraction was washed once with 100 μl Buffer B. DNase I solution (50 μl) containing DNase I (10 units; Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and SUPERase•IN RNase Inhibitor (20 units) was added to the pellets. The samples were incubated for 30 min at 37°C while being pipetted up and down several times every 10 min. QIAzol (700 μl) was then added and the solution was thoroughly mixed. RNA was extracted with an miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. On-column DNase I digestion was carried out with an RNase-free DNase set (QIAGEN). RNA was eluted in 30 μl RNase-free water, and its quality and quantity were measured with Qubit RNA HS assay kit (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent). cDNA was synthesized from 200 ng nascent RNA.
CAGE libraries were generated according to the no amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) protocol (Murata et al., 2014) with PCR amplifications (Takara, R060A).

tag: cell type

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

tag: strain


title: 523_S2-RIP_3


title: 530_S2-RIP_2


title: Col-0_0h_rep4

description: SAMPLE 4


title: 523_S2-RIP_1


title: GSCLC_1

description:
GSCLC_1.mcool
GSCLC.10kb.fanc
GSCLC.compscore.bw
GSCLC_TAD.bed

library_source: genomic

molecule: genomic DNA

source_name: GSCLC

value: GSCLC

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: GSC_2

description:
GSC_2.mcool
GSC.10kb.fanc
GSC.compscore.bw
GSC_TAD.bed

source_name: GSC

value: GSC


title: d4c7PGCLC_netcage_1

description: nascent RNA


title: d4c7PGCLC_2

description:
d4c7PGCLC_2.mcool
d4c7PGCLC.10kb.fanc
d4c7PGCLC.compscore.bw
d4c7PGCLC_TAD.bed


title: GSC_1

description:
GSC_1.mcool
GSC.10kb.fanc
GSC.compscore.bw
GSC_TAD.bed


title: EpiLC_netcage_1

description: nascent RNA

source_name: EpiLC

value: EpiLC


title: 521_S2-RIP_1


title: ESC_netcage_2

description: nascent RNA

source_name: ESC

value: ESC


title: EpiLC_netcage_2

description: nascent RNA


title: 510_S2-RIP_1


title: Col-0_0h_rep2

description: SAMPLE 2


title: ESC_netcage_1

description: nascent RNA


title: 504_S2-RIP_1


title: 504_S2-RIP_2


title: GSCLC_ATAC_2

description:
GSCLC_idr_peaks.bed
Illumina NextSeq 500 and NextSeq 550

data_processing:
ATAC-seq data processing including public data was performed as previously described (Buenrostro et al., 2013) with minor modifications. First, adaptor sequences were trimmed from the reads using trim galore!.
These reads were aligned using Bowtie2 v2.3.4.1 to GRCm38p3 with the “--very-sensitive -X 2000” option.
The properly mapped reads with the flag (99, 147, 83 or 163) were extracted by awk, and mitochondrial reads were excluded.
Duplicated reads were removed using MarkDuplicates command of Picard Tools v2.18.23.
These de-duplicated reads were then filtered for high quality (MAPQ≧30).
The reads whose insert size was less than 100 bp were extracted as nucleosome free region (NFR) reads.
Bed files for downstream analysis were generated by the bamtobed command of BEDTools v2.29.2 with the “-bedpe” option.
Peak calling was performed using MACS v2.1.1 with the “--nomodel --shift -100 --extsize 200 --keep-dup all” option after shifting NFR reads with the offset by +4bp in the + strand and by -5bp in the - strand.
Then, confident peak sets in each cell type were obtained by IDR method (https://www.encodeproject.org/software/idr/) using two replicates.
Genome_build: mm10
Supplementary_files_format_and_content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” option of deepTools v3.5.0. The blacklist regions (https://www.encodeproject.org/files/ENCFF999QPV/)  were excluded.
Supplementary_files_format_and_content: bed files contain peaks defined by MACS2 followed by IDR method.

extract_protocol:
ATAC-seq experiment was performed as described previously (Corces et al., 2017; Buenrostro et al., 2013) with minor modifications. We used FACs-sorted viable cells for mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs, d4 mPGCLCs, and d4c7 mPGCLCs, and FACS-sorted AAG-positive cells for GSCs and GSCLCs. 50,000 cells were permeabilized in cold lysis buffer 1 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin (Promega)) for 3 min followed by addition of 1 ml of cold lysis buffer 2 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20). Nuclei were centrifuged and resuspended with a 50 ul of transposase reaction mixture (25 ul of 2xTD buffer (Illumina, 20034197), 2.5 ul of Transposase (Illumina, 20034197), 16.5 ul of PBS, 0.5 ul of Digitonin, 0.5 ul of Tween-20, 5 ul of DDW). After incubation at 37°C for 30 min, the tagged DNA was purified using the Minelute PCR purification kit (QIAGEN).
The purified DNA was amplified 8 cycles by a PCR reaction (NEB, M0541S) followed by size selection using AMPure XP beads (Corning) to remove primer dimers.


title: d2PGCLC_2

description:
d2PGCLC_2.mcool
d2PGCLC.10kb.fanc
d2PGCLC.compscore.bw
d2PGCLC_TAD.bed


title: d2PGCLC_1

description:
d2PGCLC_1.mcool
d2PGCLC.10kb.fanc
d2PGCLC.compscore.bw
d2PGCLC_TAD.bed


title: GSC_ATAC_2

description:
GSC_idr_peaks.bed
Illumina NextSeq 500 and NextSeq 550


title: GSCLC_ATAC_1


title: 491_S2-RIP_3


title: EpiLC_2

description:
EpiLC_2.mcool
EpiLC.10kb.fanc
EpiLC.compscore.bw
EpiLC_TAD.bed


title: GSC_ATAC_1


title: 491_S2-RIP_2


title: cap-h2-2_0h_rep1

description: SAMPLE 5


title: Col-0_0h_rep3

description: SAMPLE 3


title: 491_S2-RIP_1


title: EpiLC_ATAC_2

value: DBA/2 x C57BL/6


title: Col-0_0h_rep1

description: SAMPLE 1


title: ESC_1

description:
ESC_1.mcool
ESC.10kb.fanc
ESC.compscore.bw
ESC_TAD.bed


title: d4c7PGCLC_1

description:
d4c7PGCLC_1.mcool
d4c7PGCLC.10kb.fanc
d4c7PGCLC.compscore.bw
d4c7PGCLC_TAD.bed


title: crwn1/4_rep2

source_name: whole roots

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown on MGRL, 1.5% gellan gum medium for rwo weeks.

extract_protocol: Total RNA was extracted from whole roots of two-week-old plants using PureLink® Plant RNA Reagent (Thermo Fisher Scientific).

treatment_protocol: No treatment.

value: Normal condition

tag: ecotype


title: crwn1/4_rep3


title: d4c7PGCLC_ATAC_2


title: ESC_2

description:
ESC_2.mcool
ESC.10kb.fanc
ESC.compscore.bw
ESC_TAD.bed


title: d4c7PGCLC_ATAC_1


title: 324_S2-RIP_4


title: cap-h2-2_rep2


title: crwn1/4_rep1


title: cap-h2-2_rep1


title: cap-h2-2_rep3


title: Col-0_rep2


title: EpiLC_1

description:
EpiLC_1.mcool
EpiLC.10kb.fanc
EpiLC.compscore.bw
EpiLC_TAD.bed


title: 324_S2-RIP_1


title: 324_S2-RIP_2


title: ∆ldh1 iron unchelated, LDH_RP29

city: Singapore

first: Casandra

last: Tan

address: 60 Nanyang Drive

country: Singapore

institute: SCELSE

description:
∆ldh1 total RNA
LDH_RP29
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

data_processing:
Raw reads were quality and adapter trimmed using bbduk from BBMap tools (Version 39.79).
Trimmed reads were then mapped using bwa-mem of BWA (Version 0.7.17-r1188) with options “-T 20 -k 13” against E. faecalis OG1RF (NCBI accession: CP002621) or P. aeruginosa PAO1 (NCBI accession: NC_002516) reference genomes.
Reads mapped to predicted open reading frames were quantified using htseq-count of HTSeq (Version 0.12.4) with option “-m intersection-strict”.
Ribosomal sequences were filtered out from all data sets.
Differential gene expression analysis was performed in R using edgeR (Version 3.28.1).
Genome_build: E. faecalis OG1RF (NCBI accession: CP002621) and P. aeruginosa PAO1 (NCBI accession: NC_002516).
Supplementary_files_format_and_content: toOG1RF.txt, toPAO1.txt (Text files containing raw counts of sequencing reads for each sample mapped to E. faecalis OG1RF or P. aeruginosa PADP6.)
Supplementary_files_format_and_content: *VS*.txt (Normalized counts using edgeR for every comparison made. )
Supplementary_files_format_and_content: *conditions.txt (Sample metadata csv file used in DGE analysis in edgeR.)

organism: Enterococcus faecalis

source_name: E. faecalis ∆ldh1 macrocolonies on TSBG agar (single-species)

growth_protocol: Single-species (E. faecalis OG1RF, E. faecalis ∆ldh1 or P. aeruginosa PADP6) and mixed-species (PADP6+OG1RF or PADP6+∆ldh1) macrocolonies grown in TSBG agar (TSB supplemented with 10 mM glucose) at 37ᵒC for 48 hours.

extract_protocol:
Macrocolonies were first scraped into RNAprotect™ Bacteria Reagent and bacteria pellets were then subjected to total RNA extraction using RNeasy® mini kit with slight modifications. Briefly, cell pellets were resuspended in TE buffer containing 20 mg/mL lysozyme and further supplemented with 20 µL proteinase K. Followed by incubation at 37 °C for 1 h, and subsequent extraction steps was performed according to manufacturer’s protocol. Extracted RNA samples were treated with DNase (TURBO DNA-free™ kit, Invitrogen, USA) and purified using Monarch® RNA cleanup kit.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.

treatment_protocol: Macrocolonies were grown in TSBG agar with or without 2 mM 2,2’ bipyridyl.

tag: genotype mapped

tag: growth protocol

value: iron replete

tag: condition

value: single

tag: e. faecalis strain


title: 324_S2-RIP_3


title: 302_S2-RIP_3


title: ∆ldh1 iron unchelated, LDH_RP27

description:
∆ldh1 total RNA
LDH_RP27
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: ESC_ATAC_2


title: EpiLC_ATAC_1


title: KO Naïve #2 (17424X17)

city: Salt Lake City

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

data_processing:
The mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 98
Reference database was created using STAR version 2.7.2c with splice junctions optimized for 150 base pair reads
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using DESeq2 version 1.30.1 with a 5% FDR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts

source_name: Spleen

extract_protocol:
RNA was harvested from FACS sorted cells using Direct-zol RNA MicroPrep kit (Zymo Research).
RNA libraries were constructed using Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold (Human, Mouse, Rat)

tag: genetics

value: Tet2 KO

tag: background

value: Mouse SMARTA CD4 T Cells

tag: cell subset

value: naive

tag: infection

value: Not Infected

tag: time point

value: Naïve

value: Male


title: KO Naïve #3 (17424X18)

tag: Sex


title: WT Naïve #3 (17424X16)

value: WT


title: Col-0_rep1


title: KO Tfh #3 (17424X15)

value: Tfh

value: LCMV Armstrong

value: 7 days post infection

value: Female


title: ∆ldh1 iron chelated, LDH_DP35

description:
∆ldh1 total RNA
LDH_DP35
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

source_name: E. faecalis ∆ldh1 macrocolonies on iron chelated TSBG agar (single-species)

value: iron deplete


title: KO Th1 #3 (17424X14)


title: ∆ldh1 iron chelated, LDH_DP33

description:
∆ldh1 total RNA
LDH_DP33
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: Col-0_rep3


title: ESC_ATAC_1

value: ESC

tag: genotype

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: 302_S2-RIP_2

tag: strain number

tag: target molecule

value: RNA-PolII bound RNA

tag: ip antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: WT Tfh #3 (17424X13)

tag: cell type


title: 302_S2-RIP_1


title: ∆ldh1 iron unchelated, LDH_RP25

description:
∆ldh1 total RNA
LDH_RP25
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

value: iron replete

value: single


title: 301_S2-RIP_3


title: ∆ldh1 iron chelated, LDH_DP31

description:
∆ldh1 total RNA
LDH_DP31
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: 301_S2-RIP_2


title: WT Th1 #3 (17424X12)

value: Mouse SMARTA CD4 T Cells


title: KO Th1 #2 (17424X10)

value: Tet2 KO


title: KO Tfh #2 (17424X11)


title: OG1RF iron unchelated, EF_RP17

description:
OG1RF total RNA
EF_RP17
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

source_name: E. faecalis OG1RF macrocolonies on TSBG agar (single-species)


title: 1168_S2-RIP_2


title: OG1RF iron unchelated, EF_RP13

description:
OG1RF total RNA
EF_RP13
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: 301_S2-RIP_1


title: 1168_S2-RIP_1


title: OG1RF iron unchelated, EF_RP15

description:
OG1RF total RNA
EF_RP15
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: WT Th1 #2 (17424X8)


title: OG1RF iron chelated, EF_DP23

description:
OG1RF total RNA
EF_DP23
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

source_name: E. faecalis OG1RF macrocolonies on iron chelated TSBG agar (single-species)


title: WT Tfh #2 (17424X9)


title: 1022_S2-RIP_5


title: WT Naïve #2 (17424X7)

value: naive

value: Not Infected


title: OG1RF iron chelated, EF_DP21

description:
OG1RF total RNA
EF_DP21
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt


title: KO Naïve #1 (17424X6)

value: Naïve


title: WT Naïve #1 (17424X5)

value: WT


title: Control WT rep1

city: Cincinnati

first: Hitesh

last: Deshmukh

state: Ohio

address: 3333 Burnet Ave.

department: Neonatology and Pulmonary Biology

institute: Cincinnati Childrens Hospital Medical Center

description:
scRNAseq
matrix.mtx.gz

data_processing:
RTA2 software within the Illumina HiSeq 4000 was used for automatic basecalling.
Sequenced reads had adaptor sequence trimmed and were mapped to the rhesus macaque reference genome Mmul_10 with CellRanger 1.3 to generate count matrix files.
Cells that had <750 UMIs or >15000 UMIs, as well as cells that contained >20% reads from mitochondrial or rRNA genes were considered low quality and removed. Cells with >10% of reads from hemoglobin genes were also removed.
Putative multiplets were removed with DoubletFinder (v2.0) and genes expressed in <10 cells were removed in the final count matrix.
Genome_build: Mmul_10
Supplementary_files_format_and_content: *matrix.mtx: Raw expression matrix file
Supplementary_files_format_and_content: barcodes.tsv: Barcode file
Supplementary_files_format_and_content: features.tsv: Feature (gene) file

organism: Macaca mulatta

source_name: Pulmonary immune cells

extract_protocol:
Lungs were harvested and processed to single-cell suspension, which was then FACS purified for CD326-CD31-CD45+ cells. RNA was harvested and processed according to the standard 10X Genomics Chromium pipeline.
RNA libraries were prepared for sequencing using standard 10X Genomics scRNAseq Chromium protocols.

treatment_protocol: Neonatal rhesus macaques were either treated with an ABX cocktail (ampicillin, gentamicin, vancomycin) or control (saline) from PN1-7. A cohort of ABX-exposed neonates were also given a fecal transplant from control-exposed neonates from PN8-10. These 3 groups were then infected with a clinical isolate of Streptococcus pneumoniae (Serotype 19F) at PN14 before lung harvest 2.5 post-infection.

value: Pulmonary immune (CD326-CD31-CD45+) cells

tag: treatment

value: No ABX and no infection control

tag: age at harvest


title: Control WT rep2

description:
scRNAseq
matrix.mtx.gz


title: WT_S2-ChIP_3

source_name: wt

value: wt

value: RNA-PolII bound DNA


title: OG1RF iron chelated, EF_DP19

description:
OG1RF total RNA
EF_DP19
Efnorm_EfdepVSLDH1dep.txt, Efnorm_EF_repVSdep.txt, Efnorm_EfrepVSLDH1rep.txt, Efnorm_LDH1_repVSdep.txt, Efnorm_PAEFdepVSPALDH1dep.txt, Efnorm_PAEF_repVSdep.txt, Efnorm_PALDH1_repVSdep.txt, toOG1RFconditions.txt, ToOG1RF.txt

tag: genotype mapped

value: iron deplete


title: 1022_S2-RIP_2


title: 80_S2-ChIP_3


title: Fecal-transplant WT rep1

description:
scRNAseq
For the FT .fastq files, the 2 samples were split into 2 batches of files. E.g., FT1 is the first sample and FT2, FT3, and FT4 are all the second sample.
matrix.mtx.gz

value: ABX-treated macaques given FT from PN8-10; infected at PN14


title: No-ABX-control WT rep1

description:
scRNAseq
matrix.mtx.gz

value: Treated with control (saline) from PN1-7; infected at PN14


title: WT Tfh #1 (17424X2)

value: Tfh

value: LCMV Armstrong

value: 7 days post infection

value: Female


title: WT Th1 #1 (17424X1)

value: Mouse SMARTA CD4 T Cells


title: 80_S2-ChIP_1

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: Fecal-transplant WT rep2

description:
scRNAseq
matrix.mtx.gz


title: ABX-exposed WT rep2

description:
scRNAseq
matrix.mtx.gz

value: Treated with ABX from PN1-7; infected at PN14


title: 80_S2-ChIP_2


title: No-ABX-control WT rep2

description:
scRNAseq
matrix.mtx.gz


title: KO Th1 #1 (17424X3)

value: Tet2 KO


title: WT_S2-ChIP_1


title: CD44high-input-3 (18734X13)

data_processing:
Between 58 and 112 million paired-end Illumina sequencing reads were aligned to the mouse Mm10 reference genome using Novocraft novoalign v4.02.02, allowing for one random alignment of multi-mapping reads, and providing the adapter sequences for automatic trimming concordant with alignment
ChIP was analyzed using the MultiRepMacsChIPSeq pipeline v15.2, using options “--pe --optdist 10000 --dupfrac 0.05 --mapq 10 --cutoff 2 --peaksize 300 --peakgap 100 --species mouse --chrskip ‘chrM|PhiX’ --blacklist mm10.blacklist.bed”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file of Foxo1 peaks in activated (CD44high) CD4+ T cells
Supplementary_files_format_and_content: BigWig file of Foxo1 peaks in naïve CD4+ T cells

extract_protocol:
Sorted cells were fixed with 16% formaldehyde to a final concentration of 1% and crosslinking was stoped by the addition of glycine. Cells were sonicated in RIPA buffer then incubated with Foxo1 antibody (Cell signaling, C29H4) at 4C overnight .After washing, DNA was eluted with IP elution buffer (1%SDS/0.1M NaHCO3).Samples were purified with QiaQuick spin columns (Qiagen).
ChIP-Seq with NEBNext Ultra II DNA Library Prep Kit

value: Mouse SMARTA CD4+ CD44high T cells

tag: timepoint


title: ABX-exposed WT rep1

description:
scRNAseq
The first ABX .fastq (AB1) was split into two concurrent files (i.e. _L001_R1_001.fastq.gz and _L001_R1_002.fastq.gz are the full file together).
matrix.mtx.gz


title: CD44high-input-4 (18734X14)


title: B_DMSO_S64

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

data_processing:
BAM-formatted map files were generated using STAR version 2.7.3a with default parameters. S. pombe reads for spike-in analysis were mapped by bowtie version 1.2.2. "RNA-seq.S_cerevisiae.xlsx" is the expression matrix.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary_files_format_and_content: *.S_cerevisiae.genes.results: The expression values were estimated by RSEM v1.3.1 with the option "--estimate-rspd --strandedness reverse".
Supplementary_files_format_and_content: RNA-seq.S_cerevisiae.xlsx: Expression matrix.

organism: Saccharomyces cerevisiae

source_name: WT DMSO b

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD) at 30°C. For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. The Schizosaccharomyces pombe strain (Table S1) used for spike-in normalization in RNA-seq was grown in YES medium (0.5 % yeast extract, 3 % glucose, 150 μg ml-1 adenine, 100 μg ml-1 uracil, 100 μg ml-1 leucine, 100 μg ml-1 lysine, 100 μg ml-1 histidine) at 32°C.

extract_protocol:
Forty-five ml of S. cerevisiae cell culture (at an OD of 1.0) was harvested, washed in ice-cold RNase-free water twice, and stored at -80°C. In parallel, 5 ml of logarithmically growing S. pombe WT cells was harvested (at an OD of 0.4) for spike-in normalization, washed in ice-cold RNase-free water twice, and stored at -80°C. A cell pellet from S. cerevisiae, and one from S. pombe were combined in the same tube and allowed to thaw on ice. Thereafter, 1 ml of cold Trizol (Thermo Fisher Scientific, 15596026) and cold glass beads (Sigma, G8772) were added to just about cover the liquid. The tubes were vortexed for 8 minutes, and set on ice afterwards. One ml of cold Trizol was again added and a brief vortex was performed. The liquid was extracted to 1.7 ml Costar tubes. The samples were centrifuged at 12000 g for 10 minutes at room temperature, and supernatants were transferred to new Costar tubes. To the samples, 200 μl of chloroform was added (Sigma, 1024451000), and the tubes were shaken by hand for 15 seconds. The samples were allowed to settle for 2 minutes before being centrifuged at 12000 g for 15 minutes at 4°C. The aqueous phase was collected, and chloroform extraction was performed a second time. Thereafter, 500 μl of 2-propanol (Sigma, 1096341000) was added to the samples. The samples were inverted 7 times, and allowed to precipitate for 10 minutes at room temperature. The precipitates were pelleted at 7500 g for 5 minutes at 4°C, and the pellets were washed once with 1 ml of 70% ethanol, airdried, and resuspended in 25 RNase/DNase-free water. Twenty-five mg of extracted RNA was then treated with 10 units of DNase I (Sigma, 4716728001) for 15 minutes at room temperature. Large ribosomal rRNA molecules were then depleted from the samples using the RiboMinus™ Transcriptome Isolation Kit (Thermo Fisher Scientific, K155003) according to the manufacturer’s instructions.
Samples were then prepared for sequencing using the NEBNext Ultra II Directional RNA Library Prep (NEB, E7760S) according to the manufacturer's protocol.

treatment_protocol: For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

tag: strain

value: WT

value: G2/M-arrest, DMSO


title: Naive-input-3 (18734X10)

value: Mouse naive CD4 T cells

value: Not Infected

value: naïve


title: 1022_S2-RIP_4

value: RNA-PolII bound RNA


title: 591_S2-ChIP_1

value: RNA-PolII bound DNA


title: KO Tfh #1 (17424X4)


title: 530_S2-ChIP_2


title: A_Thiolutin_S63

source_name: WT Thiolutin a

value: G2/M-arrest, thiolutin


title: CD44high-input-2 (18734X12)


title: A_DMSO_S62

source_name: WT DMSO a


title: 638_S2-ChIP_2


title: 524_S2-ChIP_1


title: 544_S2-ChIP_1


title: CD44high-4 (18734X7)


title: 638_S2-ChIP_1


title: CD44high-input-1 (18734X11)


title: 530_S2-ChIP_1


title: Naive-input-2 (18734X9)


title: 510_S2-ChIP_2


title: 00014_200gy_juv_3

city: Pacific Grove

first: Christopher

last: Lowe

state: CA

address: 120 Oceanview Bvld

department: Biology

institute: Hopkins Marine Station of Stanford University

data_processing:
The resulting reads were mapped to the annotated S. californicum genome (v2.0) using CLC Genomics Workbench (CLC Bio)
Differential expression was conducted with DeSeq2
apeglm was used for log fold change shrinkage (Zhu, Ibrahim, and Love 2019) and vst (variance stabilizing transformation) was used for visualization (Anders and Huber 2010).
Genome_build: S. californicum genome (v2.0)

organism: Schizocardium californicum

source_name: 5 pooled juveniles

growth_protocol: Larvae were raised in 1 gallon glass jars and fed a 1:1 mix of Dunaliella tertiolecta and Rhodomonas lens

extract_protocol:
 Purified total RNA was extracted from pools of 5 animals using Qiagen RNeasy
Individually tagged libraries for RNA-seq were prepared (Nugen-Tecan Genomics Universal mRNA-seq Kit), pooled in a single lane, and 75-bp pair-reads were generated using an Illumina HiSeq2000

treatment_protocol: Larva and juvenile worms were exposed to 120 and 200 Gy of X-ray irradiation on a CellRad Faxitron source. Animals were cultured in FSW after irradiation for 3 days

tag: developmental stage

value: juveniles


title: Naive-input-1 (18734X8)


title: 504_S2-ChIP_3


title: B_Thiolutin_S65

source_name: WT Thiolutin b


title: 00010_0gy_juv_2


title: CD44high-3 (18734X6)

value: LCMV Armstrong


title: CD44high-1 (18734X4)

value: 7 days post infection


title: wing_disc_control_scrna

city: Leuven

first: Stein

last: Aerts

state: Flemish-Brabant

address: Herestraat 49

department: Department of Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed with CellRanger (v5.0.1) with default parameters and FlyBase r6.35 reference genome
scRNA data was processed using the NextFlow pipeline VSN (Flerin et al., 2021). VSN processing includes the doublet filtering using scrublet (Wolock et al., 2019) and the correction for batch effects between the runs using Harmony (Korsunsky et al., 2019). We used the following filtering parameters : minimum of 200 detected genes per cell, maximum of 15% signal of mitochondrial origin, minimum of 3 cells expressing any targeted genes.
Assembly: dm6
Supplementary files format and content: CellRanger output for each scRNA sample (control and tumor) comprising GEX features are present as TSV (barcode and features) and matrix (raw counts) format.

organism: Drosophila melanogaster

source_name: wing imaginal disc

growth_protocol: Wild-type flies were raised at 18°C at a density of 50 larvae/vial. Flies with induced Ras/Scrib tumor were raised at 25°C on a yeast-based medium under a 12h-12h day-night light cycle.

extract_protocol:
Eye-antennal discs or wing discs were dissected and transferred to a tube containing 100 µl ice cold PBS. After centrifugation at 800 g for 5 min, the supernatant was replaced by 50 µl of dispase (3 mg/ml, Sigma-Aldrich_D4818-2mg) and 75 µl collagenase I (100 mg/ml, Invitrogen_17100-017). Discs were dissociated at 25°C in a Thermoshaker (Grant Bio PCMT) for 45 min at 25°C, 500 rpm. The enzymatic reaction was reinforced by pipette mixing every 15 min. Cells were washed with 1 ml ice cold PBS and resuspended in 400 µl PBS supplemented with 0.04% BSA. Cell suspensions were passed through a 10 µM pluriStrainer (ImTec Diagnostics-435001050). Cell viability and concentration were assessed by the LUNA-FL Dual Fluorescence Cell Counter.
Single-cell libraries were generated using the 10x Chromium Single-Cell Instrument and Single Cell 3’ Gene Expression (GEX) kit according to the manufacturer’s protocol. Briefly, single cells from eye-antennal discs or wing discs were suspended in 0.04% BSA-PBS. After generation of nanoliter-scale Gel bead-in-emulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio Rad) programmed at 53°C for 45 min, 85°C for 5 min, and hold at 4°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified by PCR: 98°C for 3 min; 12 cycles of 98°C for 15 s, 67°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 14 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready library was cleaned up with SPRIselect beads.

treatment_protocol: Expression of the oncogenic driver Ras/Scrib was induced by raising the flies at 25°C

tag: tissue

value: wing imaginal disc

value: thrid instar larvae

tag: condition

value: control

value: w1118; +; rn-Gal4, UASeiger, tub-Gal80ts/TM6B


title: CD44high-2 (18734X5)

tag: background


title: 00011_0gy_juv_3


title: 504_S2-ChIP_2

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: Naive-3 (18734X3)

tag: infection


title: eye_disc_tumor_early_scrna

source_name: eye-antennal imaginal disc

value: eye-antennal imaginal disc

value: early tumor

value: y,w,eyFlp; act>y+>Gal4, UAS-GFP/UAS-RasV12; FRT82 tub-Gal80/FRT82 scrib-,e

value: Ras/Scrib induction


title: 00013_200gy_juv_2


title: Naive-2 (18734X2)

value: Mouse naive CD4 T cells

value: Not Infected


title: 504_S2-ChIP_1


title: 491_S2-ChIP_3


title: 523_S2-ChIP_1


title: Naive-1 (18734X1)

value: naïve


title: 00006_0gy_larva_3

source_name: 5 pooled larvae

value: larvae


title: wing_disc_wounded_rep1_multiome_atac

description:
REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.barcodes.tsv.gz
REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.features.tsv.gz
REW__51c215__7eeed7__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s1.matrix.mtx.gz

library_source: genomic single cell

data_processing:
Sequencing data were processed with CellRangerARC (v1.0.1) with default parameters and FlyBase r6.35 reference genome
scRNA data was processed using the NextFlow pipeline VSN (Flerin et al., 2021). VSN processing includes the doublet filtering using scrublet (Wolock et al., 2019) and the correction for batch effects between the runs using Harmony (Korsunsky et al., 2019). We used the following filtering parameters : minimum of 200 detected genes per cell, maximum of 15% signal of mitochondrial origin, minimum of 3 cells expressing any targeted genes.
scATAC data was processed using cisTopic (Bravo González-Blas et al., 2019) using 76 topics. scATAC count data were generated from a consensus set of 41,387 peaks based on peak calling from pseudobulk aggregate from scRNA clusters. We used the following filtering parameters : minimum number of fragment per cell of log10(3.5), minimum fraction of reads in CPS of 60%, minimum TSS enrichment of 2.
Assembly: dm6
Supplementary files format and content: Consensus peak set for scATAC is available as consensus_peak_set_atac.bed
Supplementary files format and content: CellRangerARC output for each multiome sample (control and wounded) comprising both ATAC and GEX features are present as TSV (barcode and features) and matrix (raw counts) format.

growth_protocol: Flies were raised at 18°C at a density of 50 larvae/vial

extract_protocol:
Control and wounded wing discs were dissected and transferred to a tube containing ice cold PBS. PBS was removed by centrifugation, tissues were flash frozen in liquid nitrogen and stored at -80°C. The following procedure was followed to extract the nuclei from the wing discs:  resuspension in 500 µl nuclei lysis buffer comprising 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA, 1 mM dithiothreitol and 1U/µl RNasin ribonuclease inhibitor (Promega) in nuclease-free water, incubation on ice for 5 min, transfer to a dounce tissue grinder tube (Merck), 25 strokes with pestle A, incubation on ice for 10 min, 25 strokes with pestle B.  The lysis was stopped by added 1 ml of wash buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1% BSA, 1 mM dithiothreitol and 1U/µl RNasin ribonuclease inhibitor in nuclease-free water. Nuclei were pelleted by centrifugation at 800 g for 5 min at 4°C and resuspended in a 1x nuclei buffer (10x Genomics) supplemented with 1 mM dithiothreitol and 1U/µl RNasin ribonuclease inhibitor. Nuclei suspensions were passed through a 40 µm Flowmi filter (VWR Bel-Art SP Scienceware). Nuclei concentration was assessed using the LUNA-FL Dual Fluorescence Cell Counter.
Single-cell libraries were generated using the 10x Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. In brief, the single nuclei of wing discs were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanolitre-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 37°C for 45 min, 25°C for 30 min and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). This was followed by a quenching step that stopped the reaction. After quenching, single-cell droplets were broken and the transposed DNA and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To fill gaps and to generate sufficient mass for library construction,  the transposed DNA and cDNA were amplified via PCR: 72°C for 5 min;  98°C for 3 min; 7 cycles of 98°C for 20 s, 63°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. The pre-amplified product was used as input for both ATAC library construction and cDNA amplification for gene expression library construction. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 7-9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC library was cleaned up with SPRIselect beads (Beckman Coulter). Barcoded, full-length pre-amplified cDNA was further amplified via PCR: 98°C for 3 min; 6-9 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 5-16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s. 72°C for 1 min; and hold at 4°C. The sequencing-ready GEX library was cleaned up with SPRIselect beads.

treatment_protocol: Overexpression of the TNF ligand egr transgene was induced by shifting the temperature to 30°C for 24h at day 7 after egg deposition

value: wounded

value: eiger induction


title: 00005_0gy_larva_2


title: wing_disc_wounded_rep2_multiome_atac

description:
REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.barcodes.tsv.gz
REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.features.tsv.gz
REW__454c70__69c6c8__Dros_rotundGAL4_GAL80ts_eiger_10x_multi_s3.matrix.mtx.gz


title: 00012_200gy_juv_1

value: juveniles


title: 00009_0gy_juv_1


title: wing_disc_wounded_rep1_multiome_rna


title: 00004_0gy_larva_1


title: 491_S2-ChIP_2

value: RNA-PolII bound DNA


title: wing_disc_control_rep1_multiome_atac

description:
REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.barcodes.tsv.gz
REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.features.tsv.gz
REW__e37570__709b79__Dros_rotundGAL4_GAL80ts_ctrl_10x_multi_s2.matrix.mtx.gz

value: wing imaginal disc


title: KO Th1 #3 (17951X5)

data_processing:
Library strategy: Enzymatic Methyl-seq
Sequencing data quality was assessed using FastQC v0.11.4
Adapters were trimmed from the sequencing reads using Trim Galore!v0.4.4
Alignment to the mm10 reference genome was performed using Bismark v0.19.0
Deduplication was performed with deduplicate_bismark
Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome.
Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context and considered sufficient when this value was less than 3%
Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads.
CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0
This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow.
Differentially methylated regions (DMR)  were detected using Bsmooth, Bsmooth.tst and dmrFinder in the bsseq R package
Genome_build: mm10
Supplementary_files_format_and_content: BED file from Bismark Methylation Extractor

extract_protocol:
DNA was harvested from FACS sorted cells using Dneasy Blood and Tissue Kit (Qiagen). DNA inputs of 200ng were fragmented by sonication (Covaris)
Unmethylated cytosines were converted to uracils and sequencing libraries were created using the NEBNext Enzymatic Methyl Seq kit (New England Biolabs) according the manufacturer’s instructions. DNA libraries were sequenced using an Illumina NovaSeq 6000 system following the manufacturer’s protocols.

value: Tet2 KO

value: Mouse SMARTA CD4 T Cells

tag: cell subset

tag: agent

value: LCMV Armstrong

tag: time point

value: 7 days post infection

value: Female

tag: id for sequencing


title: WT Th1 #3 (17951x4)

tag: genotype

value: WT

tag: Sex


title: 00003_120gy_larva_3


title: wing_disc_wounded_rep2_multiome_rna

value: thrid instar larvae

value: w1118; +; rn-Gal4, UASeiger, tub-Gal80ts/TM6B


title: 324_S2-ChIP_3

tag: strain number

tag: target molecule

tag: ip antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: WT Tfh #3 (18010X15)

tag: cell type

value: Tfh


title: KO Tfh #3 (18010X16)


title: 00002_120gy_larva_2

tag: treatment


title: 324_S2-ChIP_2


title: wing_disc_control_rep1_multiome_rna

value: control


title: 00001_120gy_larva_1

value: larvae


title: wild_type_granules_rep3_1 [rep3_wt_presorted_2_1]

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

description:
Comparison of differential expression between granule and lysate isolates was carried out in both wild_type and Δmimi mutant strain samples. Two independent comparisons were done on two different granule isolates(_1 and _2), against the same lysate isolates. Thus two DESeq result output tables are shown on different tabs of the DESeq results excel file.
processed data file:
featureCounts_count_table.tsv; DESeq_results_out_granuleVSlysate_inbothWT_andMutant.xls

data_processing:
Bases were called on an an Illumina NovaSeq platform
Within snakePipes standard RNAseq workflow (https://snakepipes.readthedocs.io/en/latest/content/workflows/mRNA-seq.html#mrna-seq), reads were aligned with STAR (Settings: --sjdbOverhang 100 --outSAMunmapped Within, otherwise default)
Within snakePipes standard RNAseq workflow, Peak-calling was carried out with Subread's featureCounts (Settings: Level : meta-feature level, Paired-end : yes, Multimapping reads : not counted, Multiple alignments : primary alignment only, Multi-overlapping reads : not counted, Min overlapping bases : 1, Chimeric reads : not counted, Both ends mapped : required)
Normalized abundance measures were obtained with DESeq2 for each relevant pairwise comparison (default settings) using an apeGLM correction
Genome_build: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 79
Supplementary_files_format_and_content: 1) raw count table as produced by featureCounts; 2) normalized abundance measures as presented in DESeq2 results tables

source_name: heads

growth_protocol: Flies were grown in 25C on standard apple juice based food. Adult flies were anesthetized with CO2 and massively decapitated in a kitchen blender (for the details of the sample preparatopn protocol see methods of this paper)

extract_protocol:
For sequencing of purified neuronal granules and corresponding tissue lysates,total RNA was isolated using TRIzol LS Reagent (Ambion 10296028) according to manufacturer's instructions.
Libraries were prepared with 100 ng of total RNA using TruSeq Stranded total RNA (Gold) (Illumina) according to manufacturer’s instructions.

treatment_protocol: untreated

value: adult

tag: genotype/variation

value: wild type (w1118)

tag: sample type

value: purified neuronal granules


title: wild_type_granules_rep3_2 [rep3_wt_presorted_2_2]

tag: developmental stage


title: wild_type_tissue_lysate_rep3 [rep3_wt_H]


title: 302_S2-ChIP_2

value: RNA-PolII bound DNA


title: KO Th1 #2 (18010X13)

tag: strain

value: Male


title: 3.4GPa_CAF_rep2

city: Urbana

first: Taher

last: Saif

state: IL

address: 105 S Mathews Ave

department: Grainger College of Engineering

institute: University of Illinois at Urbana-Champaign

description: Polystyrene cell culture dish. Elastic modulus = 3.4 GPa.

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38.13 assembly using HISAT2
Raw gene counts were calculated by HTSeq-count
Assembly: GRCh38/hg38
Supplementary files format and content: Gene counts from HTSeq-count in TSV format

organism: Homo sapiens

source_name: Colorectal cancer

growth_protocol: Human primary colorectal tumor CAFs, CAF05 (Neuromics), were maintained in VitroPlus III Low Serum, Complete medium (Neuromics) supplemented with 1% penicillin-streptomycin (Lonza).  Cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer instructions. Samples for RNA-seq were further cleaned up by RNeasy Mini Kit (QIAGEN).
RNAseq libraries were prepared with Illumina TruSeq Stranded mRNAseq Sample Prep kit (Illumina), polyadenylated mRNAs were captured with oligodT beads

treatment_protocol: CAFs were grown on polyacrylamide hydrogel (PA gel) substrates of 1 kPa, 10 kPa and 40 kPa elastic modulus. Fibronectin coating were applied on the substrates. Cell were also grown on plastic dish that has an elastic modulus of 3.4 GPa.

tag: tissue

value: Colorectal cancer

tag: cell line

value: Cancer Associated Fibroblast

value: 3.4GPa substrate stiffness


title: 491_S2-ChIP_1


title: 324_S2-ChIP_1


title: 3.4GPa_CAF_rep1


title: WT Tfh #2 (18010X12)

value: Mouse SMARTA CD4 T Cells

tag: cell subset

value: LCMV Armstrong

value: 7 days post infection


title: 302_S2-ChIP_1


title: WT Th1 #2 (18010X11)

value: WT

tag: agent


title: 301_S2-ChIP_2


title: 301_S2-ChIP_1


title: 1168_S2-ChIP_2


title: 40kPa_CAF_rep2

description: Polyacrylamide hydrogel substrate coated with human fibronectin. Elastic modulus = 40kPa.

value: 40kPa substrate stiffness


title: 40kPa_CAF_rep1


title: 10kPa_CAF_rep2

description: Polyacrylamide hydrogel substrate coated with human fibronectin. Elastic modulus = 10kPa.

value: 10kPa substrate stiffness


title: KO Tfh #2 (18010X14)

value: Tet2 KO

value: Tfh

tag: time point


title: 1168_S2-ChIP_1

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: WT Tfh #1 (18010X8)

value: Female

tag: id for sequencing


title: KO Tfh #1 (18010X10)

tag: genotype


title: KO Th1 #1 (18010X9)

tag: Sex


title: wild_type_granules_rep2_2 [rep2_wt_presorted_2_2]

value: adult

value: wild type (w1118)


title: 10kPa_CAF_rep1


title: Δmimi_tissue_lysate_rep3 [rep3_mutant_H]

value: {delta}mimi


title: Δmimi_granules_rep3_2 [rep3_mutant_presorted_2_2]

value: purified neuronal granules


title: wild_type_tissue_lysate_rep2 [rep2_wt_H]


title: wild_type_granules_rep2_1 [rep2_wt_presorted_2_1]


title: WT Th1 #1 (18010X7)


title: 1kPa_CAF_rep2

description: Polyacrylamide hydrogel substrate coated with human fibronectin. Elastic modulus = 1kPa.

value: Colorectal cancer

value: 1kPa substrate stiffness


title: Δmimi_granules_rep2_2 [rep2_mutant_presorted_2_2]


title: 1022_S2-ChIP_1

tag: strain number

value: RNA-PolII bound DNA


title: 1022_S2-ChIP_2

tag: target molecule


title: KO Naïve #3 (18010X6)

value: Mouse SMARTA CD4 T Cells

value: Naive

value: Not Infected

value: naive

value: Male


title: Δmimi_granules_rep3_1 [rep3_mutant_presorted_2_1]


title: S14

city: Grand Rapids

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

data_processing:
Adapter and quality trimming with TrimGalore (version 0.6.5)
Read quality assessment with FastQC (version 0.11.7)
Mapped with HISAT2 (version 2.0.3)
Reads overlapping Ensembl annotations (version 99) (58) were quantified with featureCounts (version 1.6.2)
Genes with low expression were filtered with the edgeR filterByExpr function in edgeR (version 4.0.3)
Differential expression analysis using the edgeR-robust method (version 4.0.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab separated text output from featureCounts with read counts per gene for each sample.

source_name: Cells grown in 3D culture

extract_protocol:
Arcturus PicoPure RNA Isolation Kit
NEBBext Ultra II RNA Library Prep kit for Illumina

value: iEc-ESC

tag: organoid type

value: Stroma

tag: stroma origin

value: Endometriosis


title: 1kPa_CAF_rep1

tag: cell type

value: Cancer Associated Fibroblast

value: WT

tag: treatment


title: WT Naïve #3 (18010X5)

source_name: Spleen


title: Δmimi_granules_rep2_1 [rep2_mutant_presorted_2_1]

value: adult

tag: genotype/variation

tag: sample type


title: S8


title: WT_pA-RNA_3

extract_protocol:
50 ml yeast cultures with an OD600 of 1.2 were cross-linked with 1% formaldehyde (Roth) for 15 min at room temperature. The reaction was quenched with 125 mM glycine for 5 min. The frozen pellet was resuspended in 500 µl lysis buffer (250 mM KCl, 1x Triton-X, 0.1% SDS, 0.1% Na-Desoxycholate, 50 mM HEPES pH 7.5, 2 mM EDTA, 2 mM EGTA, 5 mM MgCl2, 0.1% Nonidet P-40, 20% Glycerol) with 1 mM PMSF and Complete EDTA free Protease Inhibitor Cocktail (Roche). Lysis was performed with 0.25-0.5 mm glass beads (Roth) and the BioSpec FastPrep-24 bead beater (MP-Biomedicals), 8 cycles at 6.5 m/s for 30s and 3 min on ice. DNA was sheared by sonication (Bioruptor, Diagenode) 35 times for 30 s with a 30 s break. Cell debris was removed by centrifugation at 13 000 x g for 15 min. The crude lysate was normalized based on the RNA and Protein concentration (Nanodrop, Thermo Scientific) and incubated with 1.2 µg immobilized (Dynabeads Protein A, Thermo Scientific) antibody against Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam) for at least 2 h at 4°C. The resin with immunoprecipitates was washed five times with each 1 ml of lysis buffer and eluted with 150 µl of elution buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 15 min. Cross-linking was reversed at 95°C for 15 min and subsequent RNase A (Thermo Scientific) digest for 30 min followed by Proteinase K (Roche) digest for at least 2 h at 37°C. DNA was recovered by phenol-chloroform-isoamylalcohol (25:24:1, Roth) extraction with subsequent ethanol precipitation.
For sequencing, a ChIP-seq library was made using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB).

value: wt

value: p(A) RNA

tag: ip antibody


title: KO Naïve #2 (18010X4)

value: Tet2 KO

tag: strain

value: Female


title: Δmimi_tissue_lysate_rep2 [rep2_mutant_H]

tag: developmental stage

value: {delta}mimi


title: S13

value: iHUF

value: Normal


title: S2


title: WT_pA-RNA_1


title: KO Naïve #1 (18010X2)

value: Mouse SMARTA CD4 T Cells

tag: cell subset

value: Naive


title: WT_pA-RNA_2


title: wild_type_granules_rep1_1 [rep1_wt_presorted_2_1]

value: wild type (w1118)

value: purified neuronal granules


title: wild_type_granules_rep1_2 [rep1_wt_presorted_2_2]


title: S1


title: WT_pA-RNA_4


title: 80_pA-RNA_2


title: 80_pA-RNA_1


title: wild_type_tissue_lysate_rep1 [rep1_wt_H]


title: S32

value: Endometriotic


title: Δmimi_granules_rep1_2 [rep1_mutant_presorted_2_2]


title: 638_pA-RNA_2


title: S33


title: S34

value: Control


title: Δmimi_tissue_lysate_rep1 [rep1_mutant_H]


title: Δmimi_granules_rep1_1 [rep1_mutant_presorted_2_1]


title: 638_pA-RNA_3


title: 638_pA-RNA_1


title: S31

value: Endometriosis


title: wild-type_3 [C79_3]

description:
expression was assessed at specific flybase gene IDs, no differential expression was assessed
processed data file: featureCounts_count_table.txt

data_processing:
Bases were called on an an Illumina NovaSeq 6000 platform
Within snakePipes standard RNAseq workflow (https://snakepipes.readthedocs.io/en/latest/content/workflows/mRNA-seq.html#mrna-seq), reads were aligned with STAR 2.7.4a (Settings: --sjdbOverhang 100 --outSAMunmapped Within, otherwise default)
Within snakePipes standard RNAseq workflow, Peak-calling was carried out with Subread's featureCounts (Settings: Level : meta-feature level, Paired-end : yes, Multimapping reads : not counted, Multiple alignments : primary alignment only, Multi-overlapping reads : not counted, Min overlapping bases : 1, Chimeric reads : not counted, Both ends mapped : required)
Genome_build: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 79
Supplementary_files_format_and_content: Raw count table as produced by featureCounts (existence of reads for specific genes were only confirmed with this data, no quantification between groups was undertaken on this data)

growth_protocol: Flies were grown in 25C on standard apple juice based food. Adult flies were anesthetized on the CO2 pad and decapitated.

extract_protocol:
Heads were homogenized in QIAzol Lysis Reagent (QIAGEN 79306) and total RNA was extracted according to the manufacturer's instructions.
Libraries were prepared with 150 ng of total RNA using TruSeq Stranded mRNA library prep kit according to manufacturer’s instructions.

value: adults

value: wild type

tag: tissue

value: heads


title: 544_pA-RNA_2

data_processing:
Sequencing reads obtained in the poly(A) RNA sequencing (pA RNA), Pol II ChIP, nascent RNA sequencing (Pol II RIP) and total RNA sequencing experiments were mapped to the S. pombe reference genome (PomBase, release 2018) using splice-aware alignment tool STAR version 2.7.3a (Dobin et al., 2013).  Alignment of RIP-seq and RNA-seq data was performed with STAR default parameters. Unspliced alignments of ChIP-seq data was enforced through parameters ‘--alignIntronMax 1’ and ‘--alignEndsType EndToEnd’. Reads mapping to ribosomal RNA have been removed from further analysis.
Genomic read counts were obtained using a custom script that extended basic htseq-count functionality with ‘--mode intersection-strict’ option. Additionally, for RNA assays pA RNA, Pol II RIP and total RNA, we used the ‘--stranded yes’ option to disambiguate which strand reads originated from. In short, reads mapping uniquely to protein-coding genes and reads that map less than 16 times were counted and normalized by gene length and sequencing depth (TPM, Transcripts Per Million). We chose 16 (dg/dh have in 12-13 copies) as multi-mapping threshold for heterochromatic genes to eliminate low-complexity reads without discarding reads originating from heterochromatic regions. In the read counting, we did not distinguish between individual gene copies but used one representative copy to collect all reads stemming from any one copy.
Assembly: PomBase, release 2018
Supplementary files format and content: tab-delimited text files include raw counts for each sample


title: WT Naïve #2 (18010X3)

value: WT

tag: agent

value: Not Infected

tag: time point

value: naive


title: wild-type_1 [C79_1]


title: 530_pA-RNA_2

tag: genotype

value: p(A) RNA


title: INPUT

city: Guangzhou

first: KUNTAO

last: LI

address: College of Pharmacy, Sun Yat-sen University, Panyu District, Guangzhou city, Guangdong Province

country: China

institute: Sun Yan-Sen University

data_processing:
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentralto get effective reads.Genomic alignment (version from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
Effective reads form input sample can be used for RNA-seq analysis，the reads count value of each transcript was calculated by HTSeq(version:0.6.0),then estimating RPKM(Reads Per Kilobase of transcript per Million mapped reads) value.
RIPseekre(version1.18.0)wasemployedtoperformpeakcalling.ThenusingHommer(version:4.8)toannotatethePeaks.ThenucleotidesinPeaksregionwereusedfordetectionoftheconsensusmotifbyDREME(version:4.11.1)andMEME(version:4.11.1). MotifcentralenrichmentwasperformedbyCentriMo(version:4.11.1).Differential peak enrichment was determined by Pyicoenrich(version:2.0.7).
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using Kobas(version:3.0). The enriched results were restricted to GO biological process and KEGG pathway terms.The GO biological process and KEGG pathway terms with adjusted P-value <0.05 were considered to be significant, P-value was adjusted using the Benjamini-Hochberg method.
Assembly: hg19
Supplementary files format and content: RNA of binding to AUF1

source_name: cervical cancer cells

growth_protocol: Hela cells (Procell, CL-0101, China) were and grown in MEM medium (ThermoFisher, C11095500BT,USA) complemented with 10% fetal bovine serum (FBS) (ExCell Bio, FSP500, China) and 1% Penicillin-Streptomycin Solution (P/S) (Procell, PB180120, China) at a 37 °C constant-temperature incubator with 5% CO2.

extract_protocol:
RIP lysates were used to lysate the cells, and the RNA-AUF1 complex was co-precipitated by magnetic beads, and finally the RNA was purified
1. Purification of fragment RNA.  2. Perform first strand cDNA synthesis.  2. Immediate synthesis of the second strand cDNA.  3. Terminal repair.  4.Adaptor connection, fragment selection and purification.  5.PCR amplification and purification to complete library construction.  6.Agilent 2200 TapeStation conducts library quality inspection.  7. Machine sequencing on Illumina platform.

tag: cell line

value: Hela

value: cervical cancer cells


title: 544_pA-RNA_1

tag: strain number


title: WT Naïve #1 (18010X1)

tag: Sex

value: Male

tag: id for sequencing


title: wild-type rep_4

description:
expression was assessed for specific flybase gene IDs, no differential expression was assessed  expression was assessed at specific flybase gene IDs, no differential expression was assessed
processed data fiel: featureCounts_count_table

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Reads were aligned with STAR 2.6.1b (Settings: --sjdbOverhang 74 --alignIntronMax 30000, otherwise default)
Peak-calling was carried out with featureCounts (default settings) accross only 3'UTR genomic features
Genome_build: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 93
Supplementary_files_format_and_content: Raw count table as produced by featureCounts (existence of reads for specific genes were only confirmed with this data, no quantification between groups was undertaken on this data)

growth_protocol: Flies were grown in 25C on standard apple juice based food. Adult flies were snap freezed, decapitated and head powder was prepared as described in Carrasco et al., 2020. (for details of sample preparation protocol see methods of this paper)

extract_protocol:
RNA was purified with TRIzol LS Reagent (Ambion 10296028) according to the manufacturer’s instructions.
3' mRNA-seq: Libraries were prepared with 10 ng of total RNA using QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen) according to manufacturer’s instructions.


title: late db/db with intervention_scRNA-seq

city: Shanghai

first: Yan

last: Chen

address: 320 Yueyang Road

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10_Ensembl92
Supplementary_files_format_and_content: matrix.mtx.gz contain counts for each barcodes and genes;  barcodes.tsv.gz contain all barcodes;  features.tsv.gz contain all genes.

source_name: pancreas islets cells

growth_protocol: Eight-week-old male C57BL/6 mice and C57BL/ksJ-db (db/db) mice were purchased from SLAC (Shanghai, China) and were maintained in pathogen-free conditions on a 12h light/dark cycle.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: For T2D, db/db mice were fed until they became hyperglycemia (>10 mmol/l). Then all mice were weighed at the beginning of the study and randomly allocated to different experimental groups.

value: late db/db with intervention

tag: age

value: post natal day 98d


title: 530_pA-RNA_1

tag: target molecule


title: late db/db_scRNA-seq

value: late db/db


title: JNJ-1.75-1

data_processing:
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis.
Assembly: hg38
Supplementary files format and content: DEGs of each group

source_name: skin melanoma cells

growth_protocol: SK-MEL-2 cells (BIOWING, China) were and grown in MEM medium (KeyGEN, KGM41500N-500, China) complemented with 15% fetal bovine serum (FBS) (ExCell Bio, FSP500, China) and 1% Penicillin-Streptomycin Solution (P/S) (Procell, PB180120, China) at a 37 °C constant-temperature incubator with 5% CO2.

extract_protocol:
The total RNA of each group was isolated by RNAiso Plus, separately.
1. Total RNA extraction. 2. Perform first strand cDNA synthesis. 2.Proceed immediately to second strand cDNA synthesis. 3. Purifiy double-stranded cDNA using DNA clean beads. 4. End prep of cDNA library. 5. Adaptor ligation. 6. Purifiy the Adaptor Ligated DNA Using Beads. 7. PCR Enrichment of Adaptor Ligated DNA. 8. Purification of the PCR reaction using beads.

treatment_protocol: SK-MEL-2 cells were treated with 1.75 µM JNJ-7706621 or DMSO for 48 h.

tag: treatment

value: treated with JNJ-7706621 for 48 hours

tag: cell type

value: skin melanoma cells


title: AUF1

description: RNA binding to AUF1

tag: antibody

value: Anti-hnRNP D (abcam; ab61193)


title: S30

tag: organoid type

value: Control

tag: stroma origin

value: Normal


title: wild-type rep_2

tag: developmental stage

value: adults

value: wild type


title: wild-type_2 [C79_2]

tag: genotype/variation

value: heads


title: CTRL-1

value: DMSO


title: normal control_scRNA-seq

tag: sample type

value: normal control


title: 510_pA-RNA_1

value: p(A) RNA

tag: ip antibody


title: 510_pA-RNA_2


title: ΔfneΔrbp9_5

description:
raw counts per gene obtained, differential expression assessed between wild_type and ΔfneΔrbp9 samples
processed data file:
featureCounts_count_table.tsv; DESeq_results_out_fnerbp9_vs_wt.txt

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Within snakePipes standard RNAseq workflow (https://snakepipes.readthedocs.io/en/latest/content/workflows/mRNA-seq.html#mrna-seq), reads were aligned with STAR (Settings: --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within, otherwise default)
Within snakePipes standard RNAseq workflow, Peak-calling was carried out with Subread's featureCounts (Settings: Level : meta-feature level, Paired-end : yes, Multimapping reads : not counted, Multiple alignments : primary alignment only, Multi-overlapping reads : not counted, Min overlapping bases : 1, Chimeric reads : not counted, Both ends mapped : required)
Normalized abundance measures were obtained with DESeq2 for each relevant pairwise comparison (default settings) using an apeGLM correction for low read count
Genome_build: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 79
Supplementary_files_format_and_content: 1) raw count table as produced by featureCounts; 2) normalized abundance measures as presented in DESeq2 results tables

growth_protocol: Flies were grown in 25C on standard apple juice based food. One day after eclosion flies were anesthetized on the CO2 pad and decapitated.

extract_protocol:
Heads were homogenized in QIAzol Lysis Reagent (QIAGEN 79306) and total RNA was extracted according to the manufacturer's instructions.
Libraries were prepared with 725 ng of total RNA using TruSeq Stranded total RNA (Gold) (Illumina) according to the manufacturer’s instructions.

tag: tissue


title: S29


title: wild-type rep_1

tag: genotype


title: 504_pA-RNA_1

growth_protocol: Cells were grown in rich YES medium.


title: RA patient 3

city: DUBLIN, IRELAND

first: Achilleas

last: Floudas

address: Pearse street 152 - 160

country: Ireland

institute: Trinity Biomedical Sciences Institu

description: 10x Genomics

data_processing:
none provided by the submitter
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovial tissue (knee joint)

extract_protocol:
RA and PsA patients (defined by the ACR and CASPAR Criteria respectively) were recruited from the Rheumatology Department, St. Vincent’s University Hospital, UCD and Tallaght University Hospital, TCD.  RA and PsA patient synovial tissue samples from knee joints with active inflammation were obtained under local anaesthetic using Wolf 2.7 mm needle arthroscopy or ultrasound guided biopsy as previously described, please see table S1 for patient clinical characteristics 63.  RA and PsA patients had comparable moderate to high disease activity (DAS28 4.6 ± 1.1 and DAPSA 24.2 ± 4.9 respectively) and biopsies had lymphocyte infiltrates and lining layer hyperplasia as scored by a clinical pathologist. All patients gave fully informed written consent approved by the institutional Ethics Committee and research was performed in accordance with the Declaration of Helsinki.Synovial tissue single cell suspensions were generated following enzymatic and mechanical digestion of the synovial biopsies as described previously 27. Briefly, approximately 15 synovial biopsies per patient were digested using the GentleMACS Tumor Dissociation Kit, human (Miltenyi Biotech) as per manufacturers’ instructions. Immediately after isolation, biopsies are washed with RPMI (Merck) before being placed in 4.7 ml RPMI supplemented with 200 μl of enzyme H, 100 μl enzyme R and 25 µl enzyme A in a gentleMACS™ C Tube followed by initial mechanical disruption of the tissue using program h_tumor_01 on a gentleMACS™ Dissociator. Samples are enzymatically digested for a total of 1 h at 37 °C under continuous rotation using the MACSmix Tube Rotator with further applications of the gentleMACS™ Dissociator at the halfway point and at the end of the 1 h incubation. The cell suspension is then passed through a 70 µM cell strainer. Viability of the cells is assessed with trypan blue exclusion staining and immediately cryopreserved in sterile filtered 10% DMSO/FBS at a concentration of 1x10ˆ6 cells per ml.
Using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics), cells were loaded onto the GEM Chips.  The 10X Genomics Chromium Next GEM Single Cell 3’ user manual was followed for all steps to generate cDNA libraries for each sample. cDNA quantifications and quality control were determined using the Agilent TapeStation.
Final libraries were normalized, quantified (Illumina/ROX low, Kappa Biosystems), pooled based on 40k reads/sample.  Pooled libraries were sequenced on the Illumina NovaSeq using and S2 NovaSeq 6000 Reagents v1 kit and a 100-cycle sequencing run.

value: single cell suspension

value: synovial tissue (knee joint)


title: RA patient 4

description: 10x Genomics


title: RA patient 2

description: 10x Genomics


title: ΔfneΔrbp9_4


title: 491_pA-RNA_1


title: RA patient 1

description: 10x Genomics


title: ΔfneΔrbp9_3


title: 491_pA-RNA_2


title: ΔfneΔrbp9_2


title: 324_pA-RNA_4


title: ΔfneΔrbp9_1


title: wild-type rep_3


title: PSA patient 5

description: 10x Genomics


title: 324_pA-RNA_3


title: early db/db_scRNA-seq

value: early db/db

value: post natal day 70d


title: Δrbp9_5

description:
raw counts per gene obtained, differential expression assessed between wild_type and ΔfneΔrbp9 samples
processed data file:
featureCounts_count_table.tsv


title: 504_pA-RNA_2


title: Δrbp9_4


title: PSA patient 3

description: 10x Genomics


title: Δrbp9_3


title: 324_pA-RNA_2


title: PSA patient 2

description: 10x Genomics


title: PSA patient 1

description: 10x Genomics


title: 302_pA-RNA_2


title: Δrbp9_2


title: 302_pA-RNA_1


title: Δrbp9_1


title: Fbxw11 overexpressed LSK cells

city: Tianjin

first: Lina

last: Wang

address: 288 nanjing Road

institute: institute of blood disease

description: LSK form Normal BM with Fbxw11 overexpression

data_processing:
10X Genomics CellRanger version 3.0.2 were used to the basecalling.
Cell Ranger (version 3.0.2) software from 10X Genomics (http://www.10xgenomics.com) was used to aligned and quantified sequencing raw data with default parameters.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: comma separated values files include UMI values for each cell

source_name: bone marrow

extract_protocol:
manufacturer of the Chromium Single Cell 3′ Reagent Kit v2
The libraries were constructed and  sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner (sequenced by Novogene).

treatment_protocol: LSK cells were isolated from C57BL/6 mice, and the cells were infected with lentivirus expressing Fbxw11. After sorting by flow cytometry, GFP+ LSK cells were named LSK-C and LSK-F11D

value: Hematopoietic stem/progenitor cells from BM

tag: strain

value: bone marrow


title: Δfne_5

value: {delta}fne


title: 301_pA-RNA_3

tag: strain number


title: LSK cells

description: LSK form Normal BM


title: HDMB03-OTX2-KD

city: Toronto

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
cellranger v6.0.1 used to generate count matrices from fastqs.
Seurat Read10X function to generate count matrix
Assembly: Hg19 v3.0.0
Supplementary files format and content: Txt file contained count matrix from Seurat Read10X

source_name: T Milde et al., J Neurooncol 2012

growth_protocol: Tumorspheres were grown in StemPro NSC Serum-Free Medium (HDMB03), and Stem Cell media (MB3W1) on ultra-low attachment tissue culture plates

extract_protocol:
Nuclei were isolated from fresh, snap frozen tumor tissues (C Nagy et al., Nat Neurosci 2020)
Samples were loaded on the Chromium Controller in combination with the Chromium Single Cell 3' V3 and V3.1 Gel Bead and Chip kits (10X Genomics)

treatment_protocol: OTX2 levels were knocked down in HDMB03 and MB3W1 Group 3 MB cells (2X105 cells/well) as previously described (Zagozewski et al., Nature Comm, 2020; Stromecki et al., Molecular Oncology, 2018). Briefly, OTX2 was silenced using Silencer Select siRNAs 9931 or 9932 (Life Technologies) at a concentration of 30 nM. A non-silencing (scramble) served as the negative control. For RNA sequencing, OTX2 was knocked down in three independent biological replicates for each cell line and silencing was confirmed by western blot (OTX2 ab21990 (Abcam) at 1:500) 72 hours following transfection.

tag: cell line

value: Human HDMB03 group 3 medulloblastoma cell line


title: MB3W1-scramble

source_name: Dietl et al., BMC Cancer 2016

value: scramble siRNA

value: Human MB3W1 group 3 medulloblastoma cell line


title: PSA patient 4

description: 10x Genomics


title: Δfne_4


title: 301_pA-RNA_2

city: Memphis

first: Mario

last: Halic

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital


title: rpb1-1, 37°C [KJ39]

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary_files_format_and_content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option . The total hic contact number of Hi-C samples was normalized.

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. The Schizosaccharomyces pombe strain (Table S1) used for spike-in normalization in RNA-seq was grown in YES medium (0.5 % yeast extract, 3 % glucose, 150 μg ml-1 adenine, 100 μg ml-1 uracil, 100 μg ml-1 leucine, 100 μg ml-1 lysine, 100 μg ml-1 histidine) at 32°C.

extract_protocol:
Our Hi-C protocol was adapted for S. cerevisiae from ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).  Fifty ml of cell culture (at an OD of 1.0) was fixed with 3 % formaldehyde for 20 minutes at 30°C, before the reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at room temperature. Cells were washed once with 1 x PBS, before being resuspended in 5 ml pre-spheroplasting buffer (100mM PIPES (pH 9.4), 10mM DTT). The cells were incubated 5 minutes at room temperature and then pelleted (1500 g for 5 minutes at room temperature), before being resuspended in 5 ml spheroplasting buffer (50mM KH2PO4/K2HPO4 (pH 7.5), 1 M Sorbitol, 10 mM DTT). Twenty-five μl of 10 mg ml-1 100T Zymolyase (Nacalai Tesque, 07665-55) was added and cells were incubated for 15 minutes at 30°C. The spheroplasts were pelleted (500 g for 5 minutes at 4°C) and washed twice with ice-cold spheroplasting buffer (containing only 1 mM DTT). The spheroplasts were then resuspended in 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2 % Igepal CA630) supplemented with 50 μl 6 x Complete (Roche) and 3 μl protease inhibitor (Sigma, P8215), and incubated on ice for 15 minutes. The spheroplasts were pelleted (1500 g for 5 minutes at 4°C) and washed twice with 500 μl of ice-cold Hi-C lysis buffer. After the last wash step the supernatant was discarded and the spheroplasts were incubated for 6 minutes at 62°C. Thereafter sodium dodecyl sulphate (SDS) was added to a final concentration of 0.2 % and the reaction was immediately and thoroughly mixed by inversion, and thereafter incubated at 62°C for 10 minutes. After addition of 80 μl H2O, 25 μl 10 % Triton X-100 was added to quench the SDS. The reaction was mixed by inversion and incubated at 37°C for 15 minutes. Thereafter, 28 μl 10 x NEB DpnII buffer and 500 units of DpnII (NEB, R0543M) was added, and the chromatin was digested overnight at 37°C. At the end of the incubation, the reaction was supplemented with 250 units of DpnII and incubated for 1 hour at 37°C. Then, the restriction enzyme was inactivated at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps was confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014).

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively. For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes. For inactivation of RNA pol II in G2/M-arrest, temperature-sensitive rpb1-1 cells were first arrested by benomyl for 2 hours at the permissive temperature of 25°C. Thereafter, the temperature was shifted to restrictive 37°C for 2 hours.

value: G2/M-arrest, temperature shift to 37C


title: 301_pA-RNA_1


title: Δfne_3

value: adults


title: HDMB03-scramble


title: Normal_3_small

city: Hefei

first: Dahai

last: Zhao

state: Anhui

address: Furong Road, 678

department: Respiratory and Critical Care Medicine

institute: The Second Affiliated Hospital, Anhui Medical University

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (grcm38) and calculate the gene expression level which was normalized to FPKM.
the find_circ software (v 1.2) was utilized to predict the junction of circRNAs.
Assembly: hg19
Supplementary files format and content: circRNA junction counts
Supplementary files format and content: raw counts

source_name: Human blood

extract_protocol:
The peripheral blood samples and TRizol reagent(Invitrogen, USA) are evenly mixed in a ratio of 1:3, total of 12 ml. Total RNA was extracted by using Trizol reagent according to the manufacturer’s instructions.
Whole transcriptome libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, United States), according to the manufacturer’s instructions. In brief, 10 mg total RNA was depleted rRNA with an Illumina Ribo-Zero Gold kit and purified for end repair and 50-adaptor ligation. Then, reverse transcription was performed with random primers containing 30 adaptor sequences and randomized hexamers. Finally, the cDNAs were purified and amplified with thermo cycler. The PCR products of 300–500 bp were purified, quantified and stored at -80℃ before sequencing. The libraries were subjected to 151 nt paired-end sequencing with an Illumina Novaseq 6000 system (Novogene, China).For small RNA (sRNA) sequencing, eight sRNA libraries were generated with TruSeq small RNA (Illumina, United States) according to the manufacturer’s instructions. Then the prepared libraries were sequenced with an Illumina Novaseq 6000 system (Novogene, China).

value: Normal human blood


title: rpb1-1, 37°C [KJ38]


title: 324_pA-RNA_1


title: Δfne_2

value: heads


title: WT, 37°C [KJ37]

source_name: WT


title: 1168_pA-RNA_2


title: Normal_2_small


title: 1168_pA-RNA_1


title: 1022_S2-RIP_3

value: RNA-PolII bound RNA

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade (ab5095, abcam)


title: Δfne_1


title: MB3W1-OTX2-KD


title: Normal_1_small


title: KTFAKWT5_FAKi

city: La Jolla

first: Duygu

last: Ozmadenci

address: Moores Cancer Center 3855 Health Sciences Drive

department: OBGYN

institute: UC San Diego

description: Total mRNA was isolated from 2 million cells

hyb_protocol: Performed according to Nanostring service.

data_processing: Data is analysed using Nsolver platform and Log2 normalized to housekeeping genes  Hdac3, Sdha, Oaz1, Sf3a3, G6pdx, Hprt, Abcf1, Tubb5, Eif2b4, Rpl19, Polr1b.

source_name: peritoneal ascites

growth_protocol: 5 million  tumor cells were intraperitoneally injected into mice and were recovered 21 days later.

extract_protocol: Total mRNA from 2 million ascites cells were isolated using invitrogen RNA extraction kit.

treatment_protocol: For FAK inhibitor or Vehicle treatments, mice were gavaged 100mg/kg twice a day,

tag: tissue type

value: ovarian cancer

value: KTFAKWT

tag: agent

value: FAKi VS4716


title: WT, 37°C [KJ36]


title: 1023_pA-RNA_2

tag: target molecule

value: p(A) RNA


title: WT, HU, aux/dox [KJ31]

tag: treatment

value: HU-arrest, auxin, doxycycline


title: wild_type_5


title: wild_type_4


title: COPD_3_small

value: Human blood with COPD


title: wild_type_3


title: WT, HU, aux/dox [KJ30]


title: COPD_2_small


title: Scc2-AID, aux/dox, thiolutin [KJ29]

value: G2/M-arrest, auxin, doxycycline, thiolutin


title: COPD_1_small


title: Scc2-AID, aux/dox, thiolutin [KJ28]


title: WT-F-6-2

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

description: High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol

data_processing:
Basecalls performed using CASAVA version 1.4
Trimming library adapters and quality controls with Trimmomatic using the following arguments; TrimmomaticPE - LEADING:25 TRAILING:25 CROP:120 MINLEN:120. Illumina adapters were removed and read pairs were trimmed to the same length
Alignement with STAR with the following arguments: --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --readFilesCommand zcat, --quantMode GeneCounts, --outFilterMultimapNmax 1.
bigwig files generated with deeptools BamCoverage
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: BIGWIG

organism: Oryza sativa Japonica Group

source_name: Seedlings

growth_protocol: 7-day-old seedlings

extract_protocol:
Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instructions
The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the HiSeq-4000 platform to generate high-quality paired-end reads.

treatment_protocol: Three hours and six hours treatment with 200mM NaCl, 4ºC and mock

tag: background

value: Oryza sativa Japonica Group cv Nipponbare

value: WT

tag: age

value: 4ºC, 6hours

value: Seedlings


title: wild_type_2


title: WT-F-6-1


title: Normal_3_lnc


title: WT-S-6-2

value: 200mM NaCl, 6hours


title: wild_type_1

value: adults


title: WT, aux/dox, thiolutin [KJ27]


title: Normal_2_lnc

value: Normal human blood


title: WT, aux/dox, thiolutin [KJ25]


title: WT, aux/dox, DMSO [KJ26]

value: G2/M-arrest, auxin, doxycycline, DMSO