title: Jurkat - Medium pool - repl 2

city: La Jolla

first: Graham

last: McVicker

state: CA California

address: 10010 N Torrey Pines Rd

department: Integrative Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
Library strategy: guide sequencing (CREST-seq)
Guide pairs overlapping structural variants (homozygous deletions, translocation, inversions, long deletions, long insertions, short deletions and short insertions, detected by Gioia et al., 2018.) were removed from the list of total guide pairs. Guide counts were obtained by aliging reads to guide constructs bsaed on filtered guide list. Guide 1 constructs were created by GGAAAGGACGAAACACC + guide 1 + GTTTAAGAGCTATGCTGGAAACAGCATAGCAAGT. Guide 2 constructs were created by TGCTATTTCTAGCTCTAAAAC + guide 2 + AAGGTGGTTCTCCAAGGGATACTTATAG. Each alignment was required to have at least 60 matches (column 6 of .sam file). Incorrect guide pair aignments due to guide swapping were removed.
RELICS (Fiaux PC et al., 2020) was used to discover functional sequences based on filtered guide pairs (see GATA3_filtered_guide_count.txt). Default RELICS+ paramters were used.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include all guide pairs
Supplementary_files_format_and_content: tab-delimited text files include filtered guide pairs
Supplementary_files_format_and_content: tab-delimited text files include guide counts for filtered guide pairs of all 24 pools

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured at 37 celsius degree in 5% CO2, in RPMI-1640 medium (Gibco) supplemented with 5% fetal bovine serum (FBS, Gemini).

extract_protocol:
To extract genomic DNAs, 0.5 million cells were incubated with 20 ml, 10 mg/ml proteinase K (SIGMA-ALDRICH INC, P8044) in 300 ml cell swelling buffer (10mM Tris-HCl, pH 8.0, 85mM KCl, 0.5% NP-40, and 10mM MgCl2) at 55 °C overnight. Genomic DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (Life Technologies #15593031) and ethanol precipitation.
The gRNA inserts were amplified from genomic DNA from multiple PCR reactions, in which 400 ng gRNA DNA was used in one single PCR reaction. For example, if there were a total 12 mg genomic DNA in one pool, 30 PCR reactions were performed using Herculase II fusion DNA polymerase (AGILENT TECHNOLOGIES, #600679) for 3 cycles to amplify guide insert and add Illumina TruSeq sequencing adaptors. For each pool, the amplified guide inserts from multiple PCR reactions were pooled together and purified by AMPure XP beads (BECKMAN COULTER). A second PCR was performed to add TruSeq sequencing primers (Forward primer: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTctTGTGGAAAGGACGAAAC; Reverse Primer: CAAGCAGAAGACGGCATACGAGATAAGGCCACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttttAACTTGCTATTTCTAGCTCTAAAAC) to the purified guide inserts for 16 cycles, with 400 ng/PCR reaction. The final guide libraries were sequenced using an Illumina NextSeq instrument in pair-end mode with 75 bp read length.

treatment_protocol: Regular Jurkat culture without any special treatment

tag: cell type

value: Jurkat cells

tag: cell population

value: Cas9+ Jurkat cells sorted into GATA3 medium expression pool


title: Jurkat - High pool - repl 2

status: Public on Feb 24 2023

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: Cas9+ Jurkat cells sorted into GATA3 high expression pool


title: Jurkat - Bulk pool - repl 2

value: Sorted Cas9+ Jurkat cells seqeunced to capture guide-pair distribution


title: Jurkat - Medium pool - repl 1


title: i1_NHS_IgG_rep1

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

description:
nascent RNA
iPRO_NHS_IgG_BRs_normalized_pl.bigWig
iPRO_NHS_IgG_BRs_normalized_mn.bigWig

library_source: transcriptomic

data_processing:
The reads were sorted into distinct samples using fastx barcode splitter (http://hannonlab.cshl.edu/fastx_toolkit/).
For paired-end reads, the R1 and R2 reads were paired using fastq_pair (https://github.com/linsalrob/fastq-pair). Reads from multiple sequencing runs (re-sequencing) were combined.
The adapter sequences were removed and UMI indicated in fastp (Chen et al., 2019).
The reads were mapped to mm10 spike-in genome (masked not to recognise run-on reads from the human genome) using Bowtie2 (Langmead and Saltzberg, 2012)
The reads were mapped to hg19 using Bowtie2 (Langmead and Saltzberg, 2012), and sam files converted to bam files with samtools (Danecek et al., 2021).
bed files and begraph files were generated using bedtools (Quinlan and Hall, 2010).
BigWig files were generated using bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Normalized, replicate-combined bigWig files are provided.

molecule: total RNA

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
Chromatin isolation: Cells were transferred into a large volume of ice-cold PBS to instantly bring the temperature below 8°C. The cells were pelleted by centrifugation and washed with ice cold PBS. The cell pellets were resuspended in ice-cold NUN buffer and the samples vortexed and centrifuged at 12 500 G at 4°C for 30 minutes. The chromatin pellet was washed once in ice cold 50 mM Tris-HCl (pH 7.5) and stored at -80°C.
PRO-IP-seq: Fragmented chromatin was subjected to a run-on reaction with biotinylated rA/rC/rG/rUTP. After the run-on reaction the samples was divided into distinct tubes for antibody-specific immunoprecipitation. After 3'-ligation of barcoded adapters (6nt barcode + constant G at the ligation site), the samples were re-pooled into a single tube. The nascet RNA was selected with streptavidin beads (x3 during the PRO-IP-seq protocol). The 5'-ends of nascent transcripts were decapped, repaired and ligated to UMI-containing adapters (6-nt UMI + constant C at the ligation site). The nascent RNA was reverse-transcribed, quality controlled and amplified to final sequencing library (Illumina TruSeq small RNA).
Illumina NextSeq 500 and Illumina NovaSeq6000

treatment_protocol: The cells were maintained at 37°C (NHS) or heat treated for 30 min at 42°C (HS30). The heat shock was conducted in pre-conditioned pre-warmed media. The control cells (NHS) were treated as the heat shocked (HS30) cells but using preconditioned media pre-warmed to 37°C.

tag: protocol

value: No heat shock, maintained at 37degreeC (NHS)

tag: antibody

value: SantaCruz sc2027

tag: antibody epitope

value: unspecific IgG

tag: library preparation

value: PRO-IP-seq


title: Jurkat - Low pool - repl 2

value: Cas9+ Jurkat cells sorted into GATA3 low expression pool


title: Jurkat - Bulk pool - repl 1


title: Jurkat - Low pool - repl 1


title: Jurkat - High pool - repl 1


title: Jurkat - Medium pool - repl 4


title: Jurkat - Med.-Low pool - repl 4

value: Cas9+ Jurkat cells sorted into GATA3 medium-low expression pool


title: Bladder_tumor_S3_exp1 short-term

status: Public on Feb 25 2023

type: RNA

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

description: Gene expression data from MB49-induced murine bladder cancer

hyb_protocol: 15ug cRNA was used for 2nd-cycle ss-cDNA of which 3ug cDNA was fragmented and hybridized onto Mouse Clariom S HT 24-array plates.

scan_protocol: Scanning was done using the GeneTitan Scanner systems (Thermo Fisher).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

label: biotin

organism: Mus musculus

source_name: Mice bladder cancer 12d 1 treatment

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the Affy WT PLUS Reagent Kit ( ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. On day 0, bladders were emptied and preconditioned by intravesical instillation of 100 μl poly-L-lysine solution (0.1 mg/ml) for 30 minutes followed by instillation of MB49 mouse bladder carcinoma cells (2 × 10^5 in 100 μl PBS).

extract_protocol: At sacrifice, bladders were aseptically harvested for mRNA extraction and and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Treatment groups received 100 μl intravesical instillations with alpha1-oleate (1.7 mM or 8.5 mM) or chemotherapeutic drugs (MMC 25 μg, Epirubicin 25 μg), alone or in combination (2 -3  hours) on days 3, 5, 7, 9 and 11. Sham treated animals received PBS and healthy mice bladders were used as control. Bladder samples were collected after 12 days and 27 days (4w, follow-up).

tag: gender

value: female

tag: mouse strain

tag: tissue

value: bladder

tag: experiment

tag: treatment

value: Epi


title: Jurkat - Med.-High pool - repl 4

value: Cas9+ Jurkat cells sorted into GATA3 medium-high expression pool


title: ChIPseq_GRHL2_H9_day7_rep2

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: H9 day7

growth_protocol: Human embryonic stem cells (H9, female) were maintained in E8 medium (Life Technologies) on Matrigel (Stem Cell Technologies) coated plates, dissociated using 0.5mM EDTA, and passaged at 1:10 ratio.

extract_protocol:
Cells were grown on 15-cm dishes (25 million cells per replicate), singularized by Accutase (Innovative Cell Technologies), crosslinked by 1% formaldehyde for 10 minutes, lysed (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1X protease inhibitors), and sonicated to 200-300 bp size using a Bioeruptor (Diagenode). Samples were centrifuged to remove insoluble debris and diluted in dilution buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1X protease inhibitors) to final concentration of 0.1% SDS.
Sheared chromatin was incubated overnight at 4°C with appropriate antibodies, followed by incubation on rotator with 30μL of pre-washed agarose G beads (Invitrogen) for 4h at 4°C. AP2A ChIP antibody (Santa Cruz: sc-12726) used at 20μg per 25 million cells and GRHL2 ChIP antibody (Sigma Prestige: HPA004820) used at 6μg per 25 million cells. Beads were washed twice each with low salt buffer (50 mM Tris-HCl pH 8.0, 0.15M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), high salt buffer (50mM Tris-HCl pH 8.0, 0.5M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), and LiCl buffer (50mM Tris-HCl pH 8.0, 0.15M LiCl, 1mM EDTA pH 8.0, 1% NP-40, 0.1% sodium deoxycholate). DNA was eluted in 100μL of elution buffer (50mM NaHCO3, 1% SDS) and crosslinks were reversed with 4μL of 5M NaCl incubated overnight at 67°C. RNA was removed by adding 1μL of 10 mg/mL RNase A and incubating for 30 min at 37°C. DNA was cleaned using the Qiagen Qiaquick PCR purification kit and quantified using Qubit (Invitrogen). Between 5ng and 1μg of pooled DNA were used for library preparation using NEBNext Ultra™ II DNA Library Prep Kit for Illumina kit (New England Biolabs) and AMPure XP beads (Beckman) according to the manufacturer’s protocol. Single-read libraries were sequenced on Illumina NextSeq or NovaSeq sequencer. Two independent, biological replicates were sequenced per cell type.

treatment_protocol: For differentiations, the media was changed to Essential 6 (Life Technologies) supplemented with 1μM retinoic acid (Sigma) and 5ng/mL Recombinant Human BMP4 (R&D Systems) and replaced every two days for seven days. On day 7, cells were collected for downstream analysis.

value: 7 days RA/BMP4

tag: chip antibody

value: GRHL2, Sigma, AB_1857928


title: Jurkat - High pool - repl 4


title: Jurkat - Low pool - repl 4


title: ATACseq_d7_AP2A_KO_r1

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
bedtools2.27.1 multicov to generate normalized counts
DESEQ2 used for differential peak calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
ES cells were removed from the tissue culture plate and singularized by Accutase treatment.
ATAC-seq was performed as described previously (Buenrostro et al., 2015). Briefly, 7x104 cells were washed with cold PBS and lysed in 0.1% NP40 RSB buffer. Nuclei were transposed with Nextera Transposase at 37°C for 30 minutes, then purified with the Qiagen MinElute PCR Purification Kit. Libraries were amplified for 9 total cycles using the Nextera Ad1 and Ad 2.1-2.16 barcodes. Libraries were purified and eluted using the MinElute columns (Qiagen). Library concentrations were determined with Bioanalyzer High-Sensitivity DNA analysis (Agilent). Paired-end libraries for all samples analyzed were pooled and sequenced on an Illumina NextSeq 500 and two independent, biological replicates were sequenced per sample.

tag: genotype

value: TFAP2A KO


title: i2_HS30_input_rep2

description:
nascent RNA
iPRO_HS30_input_BRs_normalized_pl.bigWig
iPRO_HS30_input_BRs_normalized_mn.bigWig

value: Heat treated at 42degreeC for 30 minutes (HS30)

value: no antibody


title: Jurkat - Bulk pool - repl 3

value: Jurkat cells


title: ChIPseq_TFAP2A_H9_day7_rep2

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Briefly, cells were detached with Accutase and crosslinked in solution for 10 minutes in freshly prepared 1% formaldehyde (Thermo Scientific) in PBS. Cell were quenched in 0.125M glycine, followed by two washes with cold PBS. 25x106 cross-linked cells were used per ChIP replicate. Cells were lysed in lysis buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1X protease inhibitors) for 30 minutes on ice and sonicated twice for 10 minutes on a Diagenode Bioruptor to achieve a chromatin between 200 and 400bp in size. Chromatin was centrifuged, quantified and diluted in dilution buffer up to 2mL (50mM Tris-HCl pH 8.0, 10mM EDTA, 1X protease inhibitors). Sheared chromatin was incubated overnight at 4°C with a TFAP2A antibody. The next day lysates were incubated with 30μL of Dynabead protein G beads (Invitrogen) for 4 hours at 4°C. Beads were washed twice each with low salt buffer (50mM Tris-HCl pH 8.0, 0.15M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), high salt buffer (50mM Tris-HCl pH 8.0, 0.5M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), and LiCl buffer (50mM Tris-HCl pH 8.0, 0.15M LiCl, 1mM EDTA pH 8.0, 1% Nonidet P-40, 0.1% sodium deoxycholate). DNA was eluted in 100μL of elution buffer (50mM NaHCO3, 1% SDS) and crosslinks were reversed with 4μL of 5M NaCl incubated shaking for 16 hours at 67°C. RNA was removed by adding 1μL of 10mg/mL RNase A for 30 minutes at 37°C. DNA was cleaned using the Qiaquick PCR purification kit (Qiagen) and quantified using Qubit (Invitrogen).
10ng of DNA was used to make libraries with the NEBNext kit (New England Biolabs) and AMPure XP beads (Beckman Coulter) according to the manufacturer instructions.

tag: cell line


title: Jurkat - High-Low pool - repl 4

value: Cas9+ Jurkat cells sorted into GATA3 high-low expression pool


title: Jurkat - High-High pool - repl 3

value: Cas9+ Jurkat cells sorted into GATA3 high-high expression pool


title: Jurkat - Low pool - repl 3


title: Jurkat - High-Low pool - repl 3


title: Jurkat - Bulk pool - repl 4

value: Sorted Cas9+ Jurkat cells seqeunced to capture guide-pair distribution


title: Jurkat - High pool - repl 3

value: Cas9+ Jurkat cells sorted into GATA3 high expression pool


title: Jurkat - Medium pool - repl 3

value: Cas9+ Jurkat cells sorted into GATA3 medium expression pool


title: Input_2AKO_day7


title: ChIPseq_TFAP2A_H9_day7_rep1


title: OVCAR3_Chito

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

data_processing:
FastQ files were aligned to the hg38 human reference genome using Bowtie
‘eXpress’ software package was used to guide downstream specific analysis and derive count data
DEseq2 was used to detect significantly modified transcripts
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including per sample: transcript ID, effective counts and FPKM

source_name: OVCAR3 cells grown in the presence of chitosan coated selenium nanoparticles

growth_protocol: SKOV-3 / OVCAR-3 cells were grown in conventional flasks then trypsinized and planted in Spheroid Growth ULA 96 wells plates from Corning at 5000 cells per well

extract_protocol:
After 24h of treament, spheroids were pooled and washed 2 times in PBS before extraction of the RNA. Total RNA extraction was performed using Trizol following Qiagen RNAeasy protocols.
cDNA libraries were prepared at the 'Institut de Genomique Fonctionnelle de Lyon' using the SENSE mRNA-Seq Library Prep Kit V2 (A01160)

treatment_protocol: After 24h of growth, cells were treated with sublethal doses of selenite or coated selenium nanoparticles for 24h

value: chitosan coated selenium nanoparticles


title: SKOV3_Chito

source_name: SKOV3 cells grown in the presence of chitosan coated selenium nanoparticles


title: OVCAR3_Se

source_name: OVCAR3 cells grown in the presence of selenite

value: Sodium selenite


title: OVCAR3_Control

source_name: OVCAR3 cells grown on conditioned media

value: Control


title: OVCAR3_BSA

source_name: OVCAR3 cells grown in the presence of BSA coated selenium nanoparticles

value: BSA coated selenium nanoparticles


title: SKOV3_BSA

source_name: SKOV3 cells grown in the presence of BSA selenium nanoparticles


title: Jurkat - Med.-High pool - repl 3


title: Jurkat - Med.-Low pool - repl 3

value: Cas9+ Jurkat cells sorted into GATA3 medium-low expression pool


title: Input_H9_day7


title: SKOV3_Se

source_name: SKOV3 cells grown in the presence of selenite


title: SKOV3_Control

source_name: SKOV3 cells grown on conditioned media


title: Jurkat - High-High pool - repl 4


title: VDJ_skin_Winkler_gd

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str 1

country: Germany

institute: Hannover Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
none provided
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gamma delta T cells

extract_protocol:
Mouse ears separated into dorsal and ventral halves and digested in RPMI medium with collagenase IV and DNase I at 37 °C. Cells were filtered and further enriched using a Percoll gradient. Cells from skin preparations were further barcoded with antibody hashing (Biolegend) for the respective genoytpes according to manufacturer’s protocol (0,1µg/1*10^6 cells in 100 µl). In total , 19 mice were pooled,  7 of which were marked with Hashtag#1 as TCR𝛿-WT mice and 12 with Hashtag#2 as TCR𝛿-KI mice. γδ T cells were identified and FACS-sorted as DAPI-TCR𝛽-CD3+TCR𝛿+ and used for the 10X workflow. The pooled samples were then subjected to transcriptome and VDJ repertoire sequencing. Small intestines were removed and cleaned of connective tissue, Peyer's patches and luminal content. Intraepithelial cells were isolated by incubating in an EDTA-containing buffer at 37 °C and subsequent vigorous shaking and further enriched using a Percoll gradient. Cells from IELpreparations were further barcoded with antibody hashing (Biolegend) for the respective genoytpes according to manufacturer’s protocol (0,1µg/1*10^6 cells in 100 µl). In total , 19 mice were pooled,  7 of which were marked with Hashtag#1 as TCR𝛿-WT mice and 12 with Hashtag#2 as TCR𝛿-KI mice. γδIELs were identified and FACS-sorted as DAPI-TCR𝛽-CD3+TCR𝛿+ and 10,000 cells from TCR𝛿-WT TCR𝛿-KI each were used form the 10X workflow. The pooled samples were then subjected to transcriptome and VDJ repertoire sequencing.
After sorting, viable cell numbers were determined and subjected to 10X library preparation (Next GEM Single Cell 5’ Lib Kit V1.1) according to the manufacturer’s protocol using the 10X Chromium device. After generation of full length 10X barcoded cDNA, a part of the cDNA library was subjected to enrichment amplification of V(D)J transcripts according to manufacturer’s protocol with custom primers for TCRγ (round 1: TCRG_Cg1_2_Outer, TCRG_Cg3_Outer, TCRG_Cg4_Outer at 10mM concentration, round 2: TCRG_Cg1_3_Inner, TCRG_Cg4_Inner at 20mM concentration) and TCRδ (round 1: TRD_Outer at 10mM concentration, round 2: TCRD Inner at 20mM concentration) constant regions. The 5’GEX library was consequentially sequenced on a HiSeq platform with 100/8/100 bp and 28/9/91 bp parameters. The corresponding VDJ library was run twice on a HiSeq platform with 100/8/100 bp parameters.

value: gamma delta T cells

value: skin

tag: age

value: 6-16 weeks old


title: VDJ_IEL_Winkler_gd

description: 10x Genomics

value: SI-IEL


title: surface_skin_Winkler_gd

description: 10x Genomics


title: GEX_IEL_Winkler_gd

description: 10x Genomics


title: GEX_skin_Winkler_gd

description: 10x Genomics


title: Y4 6.9 48hrs [706-506Y46.948]

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Alignment and gene counting was performed using Kallisto (version v0.46.1; Pachter Lab)
Assembly: Mouse genome version 10 (mm10)
Supplementary files format and content: Raw count matrix of all samples

source_name: Bone Marrow

growth_protocol: HSCs were sorted from 8 to 12 weeks young B6.SJL mice. They were cultured in IMDM + 10% FBS  or in media pre-calibrated for distinct pH 6.9 + Cytokines mSCF,GCSF,mTPO 50ng/ml con at 37°C (5% CO2, 3% O2).

extract_protocol:
100 LT-HSCs were sorted and processed as recommended by Clontech SMART-Seq v4 Ultra Low Input RNA Kit. The kit generates Illumina compatible RNA-Seq Libraries
The amplified cDNA generated were used to make libraries using Illumina’s Nextera XT DNA Library Preparation kit (Catalog # FC-131-1096) as per Illumina’s instruction. The generated libraries were quantified using agilent bio-analyzer, pooled and subjected to next generation sequencing in Hi-Seq 2500, for pair end 75bp sequencing condition.
Libraries generated are Illumina platform compatible.

value: Bone Marrow

value: HSC

value: c57 B6 WT

value: pH 6.9 cultured 48 hours


title: Y5 6.9 48hrs [705-507Y56.948]


title: Y3 6.9 48hrs [705-506Y36.948]


title: Y2 6.9 48hrs [706-505Y26.948]


title: Y1 6.9 48hrs [705-505Y16.948]


title: Y6 6.9 48hrs [706-507Y66.948]


title: Y6 7.4 48hrs [708-507Y67.448]

value: pH 7.4 cultured 48 hours


title: Y4 7.4 48hrs [708-506Y47.448]


title: Y5 7.4 48hrs [707-507Y57.448]


title: Y3 7.4 48hrs [707-506Y37.448]


title: Y2 7.4 48hrs [708-505Y27.448]


title: Y1 7.4 48hrs [707-505Y17.448]


title: Y6 7.4 M [702-507Y67.4M]

value: pH 7.4 fresh uncultured control


title: Y3 7.4 M [701-506Y37.4M]


title: Y4 7.4 M [702-506Y47.4M]


title: surface_IEL_Winkler_gd

description: 10x Genomics


title: Y5 7.4 M [701-507Y57.4M]


title: Y2 7.4 M [702-505Y27.4M]


title: upf1KO.no treatment,rep1

city: Beijing

first: Yuanhao

last: Meng

state: Beijing

address: China Agricultural University (West Campus), No. 2, Yuanmingyuan West Road

country: China

institute: China Agricultural University

data_processing:
Fastqc was used to detect the quality of sequencing data,
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Hisat2 (version 2.2.1) was used as the aligner to map the reads to the reference genome [N. crassa OR74A (NC12)]
FeatureCounts (subread, version 2.0.1) was used to count the reads
Assembly: NC12
Supplementary files format and content: TXT,Text file, Recording the gene expression data of each sample

organism: Neurospora crassa OR74A

source_name: Mycelium

extract_protocol:
Total RNA was extracted by Trizol (water saturated phenol, guanidine isothiocyanate, ammonium thiocyanate, sodium acetate, glycerin) method, and then standard Illumina protocols were used to build the RNA library
Following standard Illumina protocols

treatment_protocol: The wild type and upf1 knockout strains were cultured in the same condition, with no or 20mM H2O2 treatment.

value: Mycelium

value: Hyphal cell

value: No treatment


title: mLN_pDCs_R3

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters, except for multi-mappers allowing up 10 hits in the genome and reporting only one hit in the final alignment files (outFilterMultimapNmax 10, outSAMmultNmax=1), and filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
The rsubread::featureCounts function was used to count the number of reads (5’ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: from ensembl.org, v102).
Assembly: mm10
Supplementary files format and content: counts.txt: Tab-separated text file with raw counts for Ensembl genes. Column 1 is Ensembl GeneID, Column 2 is length of all exons in nt, Column 3 and remaining columns contain raw counts.

source_name: mesenteric Lymph Nodes (mLN)

extract_protocol:
Total RNA was isolated from the indicated sort-purified cell subsets using the Ambion RNAqueous-Micro kit. RNA quality was assessed using a Fragment Analyzer.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) following manufacturer's protocols.

value: mesenteric Lymph Nodes (mLN)

value: pDCs

tag: replicate


title: mLN_cDC2_R3


title: Y1 7.4 M [701-505Y17.4M]


title: Thy_cDC2_R3

source_name: Thymus (Thy)

value: Thymus (Thy)


title: mLN_pDC_like_R3

value: pDC-like


title: mLN_cDC1_R3


title: Thy_pDCs_R3


title: Thy_pDC_like_R3


title: Thy_cDC1_R3


title: Spl_cDC1_R3

source_name: Spleen (Spl)

value: Spleen (Spl)


title: mLN_cDC2_R2


title: BM_pDCs_R3

source_name: Bone Marrow (BM)

value: Bone Marrow (BM)


title: mLN_cDC1_R2


title: BM_pDC_like_R3


title: Spl_pDC_like_R3


title: Thy_cDC2_R2


title: mLN_pDC_like_R2


title: mLN_pDCs_R2


title: Spl_pDCs_R3


title: Thy_pDC_like_R2


title: Thy_cDC1_R2


title: Thy_pDCs_R2


title: Spl_cDC1_R2


title: Spl_pDCs_R2


title: BM_pDC_like_R2


title: Spl_cDC2_R2


title: Spl_cDC2_R3


title: mLN_cDC1_R1


title: mLN_cDC2_R1


title: Thy_cDC2_R1


title: Thy_cDC1_R1


title: mLN_pDCs_R1


title: mLN_pDC_like_R1


title: Thy_pDCs_R1


title: Thy_pDC_like_R1


title: Spl_cDC2_R1


title: Spl_pDC_like_R1


title: Spl_cDC1_R1


title: BM_pDC_like_R1


title: Spl_pDCs_R1


title: BM_pDCs_R2


title: Brain [69]

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using htseq-count software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: Counts in tab-delimited text file format

source_name: Brain

extract_protocol:
Cells were directly sorted into Trizol using Fluorescence-activated cell sorting. Total RNA was extracted with the RNeasy Micro Kit and integrity was confirmed with an Agilent 2100 Bioanalyzer.
Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit. Libraries were barcoded for multiplexing. Before sequencing, library quality and concentration were measured using Qubit Fluorometric Quantitation

tag: condition

value: SUS

value: Tcells


title: Brain [70]

value: RES

tag: cell type


title: Brain [65]

value: CON


title: Brain [67]


title: BM_pDCs_R1


title: Spl_pDC_like_R2


title: mm_islets_dbdb_H3K4me1_ChIPseq_C

first: Matthew

last: Wortham

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

data_processing:
ChIP-seq: Bowtie2 v 2.2.7 was used for mapping of ChIP-seq data to the human reference genome hg19 with a seed length of 33 bp and a maximum of 2 mismatches allowed in the seed region, discarding reads aligning to multiple sites. Duplicate reads were removed using SAMtools.
ChIP-seq: Two biological replicates were used for ChIP-seq data analysis, and replicates were merged prior to analysis
ChIP-seq: Peak calling was performed using the findPeaks program of the HOMER suite of bioinformatics tools with the options -style histone, -P 0.0000001 for H3K27ac or -style factor for Lsd1 (with default P-value cutoff of P < 0.0001) with replicate-matched ChIP-seq input used as background.
mRNA-seq: mRNA-seq reads were mapped to NCBI37/mm9 (mouse) or GRCh37/hg19 (human) genomes by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files were generated from merged replicates. Peak files are provided in BED format. mRNA-seq: Cuffdiff output comparing experimental groups

source_name: Pancreatic islets

extract_protocol:
ChIP-seq: Islets were processed for ChIP immediately following isolation (for mouse islets) or shipping (for human islets). Mouse islets were hand-picked twice under a dissecting microscope to minimize acinar cell contamination. Human islets selected for ChIP-seq analysis were of > 90% purity to facilitate analysis of large quantities of islets without the need for dithizone staining. For Lsd1 ChIP, islets were transferred to complete islet media (CMRL 1066 with 13 mM glucose, 10% FBS, 2 mM L-glutamine, 100 U/mL Pen/Strep, 1 mM sodium pyruvate, 10 mM HEPES, and 0.25 mg/mL amphoterecin B) containing 1.11% formaldehyde and fixed on a rocker for 15 minutes. The reaction was quenched for 5 minutes in 0.125 M glycine. Cells were then washed in DPBS containing 0.5% NP-40 then once again in DPBS supplemented with 0.5% NP-40 and 1 mM PMSF. Islets were lysed and ChIP was performed using the ChIP-IT High Sensitivity Kit (Active Motif) with 30 μg of sheared chromatin and 4 μg anti-Lsd1 antibody (ab17721, Abcam). For histone ChIP, islets were washed once in Hanks Balanced Salt Solution (Hyclone) and then fixed for 10 min in DPBS containing 1.11% formaldehyde. Cross-linking was quenched as before, then islets were lysed by passage through a 25 gauge needle in lysis buffer (10 mM Tris-Hcl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 1% NP-40, 1% SDS, 0.5% sodium deoxycholate). ChIP was then performed as described above using 10 or 30 μg of sheared chromatin and 4 μg of anti-H3K4me1 (ab8895, Abcam) or anti-H3K27ac (39133, Active Motif) antibodies, respectively. mRNA-seq: Human islets were first treated as described under the "treatment protocol"  section above, while mouse islets were processed for RNA purification immediately following isolation. Following mouse islet isolation, islets were hand-picked twice under a dissecting microscope to minimize acinar contamination, and were then pooled from at least 2 animals per biologicla replicate. For all mRNA-seq experiments, RNA was isolated using the RNeasy Micro kit (QIAGEN) according to the manufacturer’s instructions.
ChIP-seq ibraries were constructed from purified DNA using the KAPA DNA Library Preparation Kit for Illumina (Kapa Biosystems). Input libraries were prepared from each experimental replicate using 10 ng of DNA purified immediately following shearing. Libraries were sequenced using HiSeq 4000 (Illumina). mRNA-seq libraries were prepared from 35 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with the exception of db/db mouse islets and their respective controls, from which libraries were generated with 1 μg of total RNA as described in (Xie, R. et al. Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Cell Stem Cell 12, 224-237, 2013).

treatment_protocol: Human islet mRNA-seq: Upon receipt, human islets were stained with dithizone and positively-staining material was hand-picked using a dissection microscope. Islets were allowed to recover 18-48 hours in complete media (CMRL 1066 with 13 mM glucose, 10% FBS, 2 mM L-glutamine, 100 U/mL Pen/Strep, 1 mM sodium pyruvate, 10 mM HEPES, and 0.25 mg/mL amphoterecin B) at 37°C with 5% CO2 prior to treatments. For LSD1 inhibition studies, 2 mM tranylcypromine (Sigma) was included in the culture media for 24 hours prior to analysis.

value: H3K4me1 (Abcam ab8895)

tag: treatment/condition/replicate

value: db/db recently hyperglycemic (250 mg/dL) Rep 2


title: mm_islets_dbdb_H3K4me1_ChIPseq_A

value: db/db recently hyperglycemic (250 mg/dL) Rep 1


title: Brain [68]


title: mm_islets_dbhet_H3K4me1_ChIPseq_B

value: db/+ age-matched control for db/db Rep 1


title: Brain [64]


title: Brain [63]


title: mm_islets_dbhet_H3K4me1_ChIPseq_E

value: db/+ age-matched control for db/db Rep 2


title: mm_islets_dbdb_input_ChIPseq_C


title: Brain [62]


title: Brain [61]


title: mm_islets_dbdb_input_ChIPseq_A


title: Brain [60]


title: Brain [59]


title: mm_islets_dbhet_input_ChIPseq_B


title: mm_islets_dbhet_input_ChIPseq_E


title: mm_islets_dbdb_H3K27Ac_ChIPseq_A

value: H3K27ac (Active Motif 39133)


title: mm_islets_dbdb_H3K27Ac_ChIPseq_B


title: Brain [58]


title: Brain [57]


title: mm_islets_dbhet_H3K27Ac_ChIPseq_C


title: Brain [66]


title: mm_islets_dbhet_H3K27Ac_ChIPseq_B


title: Brain [56]


title: Brain [54]


title: mm_islets_d21LSDKO_H3K4me1_ChIPseq_C

value: Wk3 Lsd1 KO Rep 2


title: Brain [55]


title: Brain [53]


title: mm_islets_d21Ctrl_H3K4me1_ChIPseq_G

value: Control for Wk3 Lsd1 KO Rep 1


title: mm_islets_d21Ctrl_H3K4me1_ChIPseq_H

value: Control for Wk3 Lsd1 KO Rep 2


title: mm_islets_d7LSDKO_H3K4me1_ChIPseq_A

value: Wk1 Lsd1 KO Rep 1


title: Brain [49]

value: Bcells


title: Brain [48]


title: Brain [50]


title: Brain [52]


title: mm_islets_d7Ctrl_H3K4me1_ChIPseq_A

value: Control for Wk1 Lsd1 KO Rep 1


title: Brain [47]


title: mm_islets_LSDKO_input_ChIPseq_B2


title: Brain [46]


title: mm_islets_d7Ctrl_H3K4me1_ChIPseq_E

value: Control for Wk1 Lsd1 KO Rep 2


title: mm_islets_Ctrl_input_ChIPseq_B2


title: mm_islets_Ctrl_input_ChIPseq_A2


title: Brain [43]


title: Tbx3-KO, 168h (AK917_S120983)

first: Michael

middle: Karl

last: Melzer

address: Albert-Einstein-Allee 23

institute: Ulm University Hospital

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.14 package DESeq2 1.34.0, running under R 4.1.3.
Assembly: UCSC mm10 based on GRCm38
Supplementary files format and content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: pancreas

extract_protocol:
RNA was isolated with the Qiagen RNeasy Mini Plus Kit.
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

value: pancreas

tag: timepoint

value: caerulein


title: Brain [45]

value: SUS


title: mm_islets_d7LSDKO_input_ChIPseq_B

value: Wk1 Lsd1 KO Rep 2


title: Brain [44]

value: CON


title: mm_islets_LSDKO_input_ChIPseq_A2

value: Wk3 Lsd1 KO Rep 1


title: Tbx3-wt, 168h (Ak914_S120991)


title: mm_islets_d21KO_H3K4me1_ChIPseq_H

value: H3K4me1 (Abcam ab8895)


title: Tbx3-KO, 168h (AK887_S120993)


title: mm_islets_d7LSDKO_H3K4me1_ChIPseq_B


title: Brain [41]


title: mm_islets_d7LSDKO_input_ChIPseq_A


title: Brain [51]


title: Tbx3-KO, 168h (AK886_S120994)


title: Tbx3-wt, 168h (AK873_S120989)


title: Brain [40]

value: RES


title: mm_islets_d7Ctrl_input_ChIPseq_B


title: mm_islets_d7Ctrl_input_ChIPseq_A


title: Brain [39]


title: Tbx3-wt, 72h (AK784_S120985)


title: Tbx3-wt, 72h (AK778_S120986)


title: Tbx3-KO, 72h (AK822_S120990)


title: Brain [38]


title: Tbx3-wt, 72h (AK776_S120984)


title: Brain [42]


title: Brain [37]


title: mm_islets_LSDKO_H3K27Ac_ChIPseq_B


title: Tbx3-KO, 72h (AK775_S120988)


title: Brain [36]


title: mm_islets_Ctrl_H3K27Ac_ChIPseq_B


title: mm_islets_Ctrl_H3K27A_ChIPseq_A


title: Tbx3-wt, 168h (AK880_S120992)


title: mm_islets_d7KO_H3K27ac_ChIPseq_H


title: Brain [35]


title: Brain [34]


title: mm_islets_d7KO_H3K27ac_ChIPseq_G


title: mBD2(SKY)-PBRM1- Replicate 2

city: West Lafayette

first: Emily

middle: C.

last: Dykhuizen

state: IN

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Data was processed and analyzed by ECLIPSEBIO
Assembly: hg19
Supplementary files format and content: BigWig files are in an indexed binary format and contain genome-wide coverage information for positive and negative strand

source_name: Renal cancer cell line

growth_protocol: Caki2 renal cancer cell lines were grown under normal conditions: McCoy's 5A with 10% FBS

extract_protocol:
Cells were UV crosslinked and processed as described in the ECLIPSEBIO RBP-eCLIP kit
Libraries were constructed according to the instructions in ECLIPSEBIO RBP-eCLIP kit
CLIP-seq

treatment_protocol: Caki2 cell line transduced with lentiviral particles for either empty vector, V5-tagged wtPBRM1 or mBD2(SKY)-PBRM1 were treated with doxycycline for 6 days for inducing protein expression

value: Caki2 with mBD2(SKY)-PBRM1

tag: antibody

value: V5 antibody (CST, #13202)


title: Fuw-CLIP- Replicate 2

value: Caki2 with Empty Vector


title: Fuw-CLIP- Replicate 1


title: wtPBRM1-CLIP- Replicate 2

value: Caki2 with wtPBRM1


title: mm_islets_LSDKO_H3K27Ac_ChIPseq_C

value: H3K27ac (Active Motif 39133)

value: Wk3 Lsd1 KO Rep 2


title: mm_islets_d7Ctrl_H3K27ac_ChIPseq_H


title: Brain [33]


title: CLIP_Input DNA- Replicate 2

value: Input


title: mBD2(SKY)-PBRM1- Replicate 1


title: CLIP_Input DNA- Replicate 1


title: Brain [32]


title: Tbx3-KO, 72h (AK777_S120987)


title: mBD2(SKY)-PBRM1-PHF10 ChIP-seq- Replicate 1

data_processing:
Data quality control, trimming and filtering were performed with Partek Flow Software Tools
ChIP-seq reads were mapped to the human (hg38) genome with bowtie2
Aligned reads were converted to bigwig format using deeptools bamCoverage
Peaks were called using MACS
Spike-in normalization was performed as described in the manuscript
Assembly: Hg38
Supplementary files format and content: BigWig files are in an indexed binary format and contain genome-wide coverage information

extract_protocol:
Cells were fixed, washed, and lysed. The chromatin was sheared using a probe sonicator and protein/DNA complexes were isolated with antibody.
Libraries were constructed using Ovation® Ultralow V2 UDI DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions. Libraries were double size selected before sequencing

treatment_protocol: Caki2 cell line transduced with lentiviral particles for either empty vector, wtPBRM1 or mBD2(SKY)-PBRM1 contsructs were treated with doxycycline for 6 days to induce protein expression

value: PHF10 Ab (Invitrogen PA5-30678)


title: wtPBRM1-PHF10 ChIP-seq- Replicate 2


title: wtPBRM1-PHF10 ChIP-seq- Replicate 1


title: Fuw-PHF10 ChIP-seq- Replicate 2


title: mm_islets_d7Ctrl_H3K27ac_ChIPseq_G

value: Control for Wk1 Lsd1 Rep 1


title: Brain [31]


title: mm_islets_10pmFast_H3K4me1_ChIPseq_D

value: Fasted (16h) Rep 2


title: Brain [30]


title: mBD2(SKY)-PBRM1-PHF10 Input DNA- Replicate 1


title: mm_islets_10pmFast_H3K4me1_ChIPseq_C

value: Fasted (16h) Rep 1


title: wtPBRM1-PHF10 Input DNA- Replicate 2


title: mBD2(SKY)-PBRM1-PHF10 ChIP-seq- Replicate 2


title: wtPBRM1-PHF10 Input DNA- Replicate 1


title: Brain [29]


title: mm_islets_10pmFed_H3K4me1_ChIPseq_D

value: Fed (4h) Rep 2


title: Fuw-PHF10 Input DNA- Replicate 2


title: Fuw-PHF10 Input DNA- Replicate 1


title: mm_islets_10pmFast_input_ChIPseq_B


title: mBD2(SKY)-PBRM1-H3K14Ac ChIP-seq- Replicate 2

value: H3K14Ac Ab (Millipore Sigma 07-353)


title: mm_islets_10pmFast_input_ChIPseq_A


title: wtPBRM1-H3K14Ac ChIP-seq- Replicate 2


title: Brain [27]

value: SUS


title: wtPBRM1-H3K14Ac ChIP-seq- Replicate 1


title: mm_islets_10pmFed_H3K4me1_ChIPseq_C

value: Fed (4h) Rep 1


title: Fuw-H3K14Ac ChIP-seq- Replicate 1


title: Brain [26]


title: Brain [28]


title: Fuw-H3K14Ac ChIP-seq- Replicate 2


title: Fuw-PHF10 ChIP-seq- Replicate 1


title: mBD2(SKY)-PBRM1-H3K14Ac Input DNA- Replicate 2


title: mBD2(SKY)-PBRM1-PHF10 Input DNA- Replicate 2


title: mBD2(SKY)-PBRM1-H3K14Ac ChIP-seq- Replicate 1


title: mm_islets_10pmFed_input_ChIPseq_B


title: mBD2(SKY)-PBRM1-H3K14Ac Input DNA- Replicate 1


title: mm_islets_10pmFed_input_ChIPseq_A


title: Brain [23]


title: wtPBRM1-H3K14Ac Input DNA- Replicate 2


title: wtPBRM1-H3K14Ac Input DNA- Replicate 1


title: mm_islets_10pmFast_H3K27Ac_ChIPseq_B


title: mm_islets_10pmFast_H3K27Ac_ChIPseq_A


title: Fuw-H3K14Ac Input DNA- Replicate 2


title: Fuw-H3K14Ac Input DNA- Replicate 1


title: Brain [25]


title: Brain [24]

value: CON


title: Brain [21]


title: mm_islets_10pmFed_H3K27Ac_ChIPseq_B


title: mm_islets_10pmFed_H3K27Ac_ChIPseq_A


title: GBM_VU39

city: Amsterdam

first: Chantal

last: Scheepbouwer

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Raw Illumina reads were first pre-processed using sRNAbench (Aparicio-Puerta et al, NAR, 2019; Aparicio-Puerta et al, NAR, 2022) for adapter removal and quality control.
The standard sRNAbench mapping step using bowtie was extended with a second round of Smith–Waterman alignment implemented using BioJava BioJava to recover additional tRNA-derived reads by further allowing gaps and/or mismatches.
Reference libraries were obtained from GtRNAdb 2.0 (Homo sapiens, GRCh38/hg38) for nuclear tRNAs and mitotRNAdb for mitochondrial tRNAs.
TRNA expression was profiled at different levels: tRNA gene level, anticodon level and amino acid level. Reads containing the 5’ end of the sequence with complete/partial or no CCA ending were classified as mature full-length transcripts.
Assembly: hg38; gtRNAdb Release 18
Supplementary files format and content: The cell lines used in this study have processed tRNA read length files in csv format. Anticodon read counts for full-length tRNA and all tRNA in .csv format are provided for all tissues used in this study.

source_name: GBM

extract_protocol:
Total RNA was extracted from various tissue samples and SU-DHL-5, SNB-75, HEK293T and hESC cell lines, using mirVana Isolation Kit. For all samples, on-column RNase-free DNase treatment was performed. Deacylation was then performed by incubating total RNA in 0.1 M Tris-HCL pH 9.0 and 1 mM EDTA for 30 minutes at 37 °C. Demethylation reaction was performed on total RNA. Briefly, 2 ug total RNA was treated with 19 uM of AlkB consisting of 8.5uM AlkB WT and 10.5 uM AlkB-D135S mutant, 10 mM KCl, 2 mM MgCl2, 283 uM freshly prepared (NH4)2Fe(SO4)2 6H2O, 0,3 mM 2-ketoglutarate, 2 mM freshly made L-ascorbic acid, 40U RNase Inhibitor and 50 mM MES buffer pH 5.0 in a total volume of 40 ul. Reactions were incubated at 25°C for 2h and quenched with 5 mM EDTA. RNA was recovered by an Oligo Clean&Concentrator-5 kit and eluted in 6 ul Nuclease-free water.
Native total RNA or demethylated total RNA was used for each cell line and tissue sample. For the workflow of ALL-tRNAseq a 5’ phosphorylated 3’ end adapter with 4 randomized nucleotides at the 5’ end and a 3’ blocking group (3C Spacer; 3SpC3, IDT) was adenylated by Mth RNA ligase and then ligated to the RNA template using a T4 RNA ligase 2, truncated KQ for 1 h at 25°C in the presence of 20% PEG. Ligated RNA was gel-purified and size-fractionated on a Novex TBE-urea 10% denaturing polyacrylamide gel to enrich small RNA molecules using two FAM-markers of 25 nt and 39 nt and an upper marker of the low range ssRNA ladder at 150 nt. Gels were stained using 1x SYBR gold nucleic acid stain in 1x TBE for 10 minutes and 3’adapter-ligated-RNA in size range of 39-150 nt were excised on a blue light transilluminator. RNA was recovered from excised polyacrylamide gel pieces by crushing the gel fragments and soaking them in 0.3M NaCl overnight at 4°C and subsequent ethanol precipitation, 5’ adapters with 4 terminal, randomized nucleotides at 3’ end were added, using T4 RNA ligase and ATP. Ligation was performed for 1h at 25°C in the presence of 20% PEG. Thereafter, reverse transcription was performed for 1h at 50°C or 42°C using SuperScript III or MarathonRT, respectively. Reactions were terminated by incubation with 0,25 M NaOH, at 95°C for 3 min, then neutralized with 0,25 M HCl. Next, cDNA was purified using MinElute Reaction Cleanup kit and PCR amplified using Phusion high-fidelity PCR master mix for 12 cycles of 98°C for 5 s, 62°C for 10s and 72°C for 10 s. A 6-nt index sequences was introduced into the adapter sequence to enable library identification from a sequenced pool. PCR products were equimolarly pooled for cluster generation without additional size-selection. Sequencing of the ALL-tRNAseq libraries was performed as single-end reads for 150 cycles on NovaSeq 6000.

tag: tissue type

value: glioblastoma (GBM)

value: demethylation


title: GBM_VU41


title: Brain [19]


title: mm_islets_input_A3

description: MsInputforLsdnew.ucsc.bedGraph.gz

value: ad libitum fed Rep 2


title: GBM_VU04


title: DLBCL_HEM26

source_name: DLBCL

value: primary Diffuse Large B-cell Lymphoma (DLBCL)


title: DLBCL_HEM13


title: DLBCL_HEM09


title: 3_Input_mouse_s2.fastq.gz

description: 3_Input_mouse_s2.fastq.gz.dir.ucsc.bedGraph.gz


title: GBM_VU06


title: mm_islets_Lsd1_ChIPseq_A

value: LSD1 (abcam, ab17721)

value: ad libitum fed Rep 1


title: DLBCL_HEM02


title: DLBCL_HEM12


title: SU-DHL-5 ALL-tRNAseq_3

data_processing:
Raw Illumina reads were first pre-processed using sRNAbench (Aparicio-Puerta et al, NAR, 2019; Aparicio-Puerta et al, NAR, 2022) for adapter removal and quality control.
The standard sRNAbench mapping step using bowtie was extended with a second round of Smith–Waterman alignment implemented using BioJava BioJava to recover additional tRNA-derived reads by further allowing gaps and/or mismatches.
Reference libraries were obtained from GtRNAdb 2.0 (Homo sapiens, GRCh38/hg38) for nuclear tRNAs and mitotRNAdb for mitochondrial tRNAs.
TRNA expression was profiled at different levels: tRNA gene level, anticodon level and amino acid level.
Assembly: hg38; gtRNAdb Release 18
Supplementary files format and content: The cell lines used in this study have processed tRNA read length files in csv format. Anticodon read counts for full-length tRNA and all tRNA in .csv format are provided for all tissues used in this study.

source_name: SU-DHL-5 cells

growth_protocol: SU-DHL-5 cells were cultured in suspension at 37°C with 5% CO2 in Roswell Park Memorial Institute (RPMI)-1640 medium. Medium was supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from various tissue samples and SU-DHL-5, SNB-75, HEK293T and hESC cell lines, using mirVana Isolation Kit. For all samples, on-column RNAse-free DNase treatment was performed. Deacylation was then performed by incubating total RNA in 0.1 M Tris-HCL pH 9.0 and 1 mM EDTA for 30 minutes at 37 °C. Demethylation reaction was performed on total RNA. Briefly, 2 ug total RNA was treated with 19 uM of AlkB consisting of 8.5uM AlkB WT and 10.5 uM AlkB-D135S mutant, 10 mM KCl, 2 mM MgCl2, 283 uM freshly prepared (NH4)2Fe(SO4)2 6H2O, 0,3 mM 2-ketoglutarate, 2 mM freshly made L-ascorbic acid, 40U RNase Inhibitor and 50 mM MES buffer pH 5.0 in a total volume of 40 ul. Reactions were incubated at 25°C for 2h and quenched with 5 mM EDTA. RNA was recovered by an Oligo Clean&Concentrator-5 kit and eluted in 6 ul Nuclease-free water.
Native total RNA or demethylated total RNA was used for each cell line and tissue sample. For the workflow of ALL-tRNAseq a 5’ phosphorylated 3’ end adapter with 4 randomized nucleotides at the 5’ end and a 3’ blocking group (3C Spacer; 3SpC3, IDT) was adenylated by Mth RNA ligase and then ligated to the RNA template using a T4 RNA ligase 2, truncated KQ for 1 h at 25°C in the presence of 20% PEG. Ligated RNA was gel-purified and size-fractionated on a Novex TBE-urea 10% denaturing polyacrylamide gel to enrich small RNA molecules using two FAM-markers of 25 nt and 39 nt and an upper marker of the low range ssRNA ladder at 150 nt. Gels were stained using 1x SYBR gold nucleic acid stain in 1x TBE for 10 minutes and 3’adapter-ligated-RNA in size range of 39-150 nt were excised on a blue light transilluminator. RNA was recovered from excised polyacrylamide gel pieces by crushing the gel fragments and soaking them in 0.3M NaCl overnight at 4°C and subsequent ethanol precipitation, 5’ adapters with 4 terminal, randomized nucleotides at 3’ end were added, using T4 RNA ligase and ATP. Ligation was performed for 1h at 25°C in the presence of 20% PEG. Thereafter, reverse transcription was performed for 1h at 50°C or 42°C using SuperScript III or MarathonRT, respectively. Reactions were terminated by incubation with 0,25 M NaOH, at 95°C for 3 min, then neutralized with 0,25 M HCl. Next, cDNA was purified using MinElute Reaction Cleanup kit and PCR amplified using Phusion high-fidelity PCR master mix for 12 cycles of 98°C for 5 s, 62°C for 10s and 72°C for 10 s. A 6-nt index sequences was introduced into the adapter sequence to enable library identification from a sequenced pool. PCR products were equimolarly pooled for cluster generation without additional size-selection. Sequencing of the ALL-tRNAseq libraries was performed as single-end reads for 150 cycles on NovaSeq 6000.

value: SU-DHL-5 cells


title: Brain [18]

value: RES


title: Brain [22]


title: mm_islets_wildtype_byUJ_ChIPseq_Lsd1

description: 7_LSD1_Chow_s_2_sequence.fastq.gz.dir.ucsc.bedGraph.gz


title: Brain [15]


title: GBM_VU62


title: GBM_VU55


title: SU-DHL-5 ALL-tRNAseq_2


title: BC-3  lytic rep-2

city: Nashville

first: John

last: Karijolich

state: TN

address: 1161 21st Ave S MCN B3301 Room / Suite A-4301, MCN B3301 Room / Suite A-4302

department: Pathology Microbiology and Immunology

institute: Vanderbilt University Medical Center

data_processing:
Raw reads quality in fastq files were assessed by FastQC
Raw reads were trimmed of adapters and aligned to the human genome (GRCh38.p13) and KSHV genome (GQ994935.1) using STAR (v2.7.3a)
Uniquely aligned reads were used as inputs to run featureCounts (v.1.5.2) to map the reads to gencode.v39 annotations. For differential gene expression, DESeq2 (v1.18.1) was run with raw read counts obtained from featureCounts.
uniquely aligned RNA reads were used as inputs for SAILOR to identify A-to-I editing sites.
Assembly: human genome (GRCh38.p13) and KSHV genome (GQ994935.1)
Supplementary files format and content: tab-delimited text files include normalized read counts values for each Sample

growth_protocol: TREx-BCBL1-PAN-GFP and BC3-PAN-GFP cells were maintained in RPMI 1640 medium (Invitrogen) supplemented with 10% FBS (Invitrogen) and 2 mM L-glutamine (Invitrogen). All cells were maintained with 100 U of penicillin/ml and 100 μg of streptomycin/ml (Invitrogen) at 37 °C under 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol and treated with DNase I. Following DNAse I treatment, RNA was recovered by extraction with phenol:chloroform:isoamyl alcohol [25:24:1 (vol/vol)] followed by ethanol precipitation.
Isolated RNA was subjected to ribosomal RNA depletion using NEBNext rRNA depletion kits (Human/Mouse/Rat: NEB E6310) according to the manufacturer’s instructions. The rRNA-depleted samples were used as the starting material to generate sequencing libraries using the NEBNext Ultra II directional RNA library prep Kit (NEB E7760) according to the manufacture recommendations.

treatment_protocol: Cells were reactivated with 2 μg/ml of doxycycline and GFP positive lytic cells were sorted using 5- laser FACS Aria III

value: B-cell lymphoma

value: WT

value: 48 hr induction with 2ug/ml Dox


title: Brain [16]


title: mm_islets_dbdb_RNAseq_C

value: db/db recently hyperglycemic (250 mg/dL) Rep 3


title: BC-3  lytic rep-1


title: Brain [20]


title: Brain [14]


title: Brain [17]


title: BC-3 latent rep-2


title: BC-3  latent rep-1


title: Trex-BCBL1 lytic rep-2

source_name: Trex BCBL1

value: Trex BCBL1


title: Trex-BCBL1 lytic rep-1


title: Brain [12]


title: Brain [13]


title: mm_islets_dbdb_RNAseq_A

value: db/db recently hyperglycemic (250 mg/dL) Rep 1


title: Trex-BCBL1 latent rep-2


title: Brain [11]

value: SUS


title: Trex-BCBL1 latent rep-1


title: i3_HS30_input_rep3

data_processing:
The reads were sorted into distinct samples using fastx barcode splitter (http://hannonlab.cshl.edu/fastx_toolkit/).
For paired-end reads, the R1 and R2 reads were paired using fastq_pair (https://github.com/linsalrob/fastq-pair). Reads from multiple sequencing runs (re-sequencing) were combined.
The adapter sequences were removed and UMI indicated in fastp (Chen et al., 2019).
The reads were mapped to mm10 spike-in genome (masked not to recognise run-on reads from the human genome) using Bowtie2 (Langmead and Saltzberg, 2012)
The reads were mapped to hg19 using Bowtie2 (Langmead and Saltzberg, 2012), and sam files converted to bam files with samtools (Danecek et al., 2021).
bed files and begraph files were generated using bedtools (Quinlan and Hall, 2010).
BigWig files were generated using bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Normalized, replicate-combined bigWig files are provided.

extract_protocol:
Chromatin isolation: Cells were transferred into a large volume of ice-cold PBS to instantly bring the temperature below 8°C. The cells were pelleted by centrifugation and washed with ice cold PBS. The cell pellets were resuspended in ice-cold NUN buffer and the samples vortexed and centrifuged at 12 500 G at 4°C for 30 minutes. The chromatin pellet was washed once in ice cold 50 mM Tris-HCl (pH 7.5) and stored at -80°C.
PRO-IP-seq: Fragmented chromatin was subjected to a run-on reaction with biotinylated rA/rC/rG/rUTP. After the run-on reaction the samples was divided into distinct tubes for antibody-specific immunoprecipitation. After 3'-ligation of barcoded adapters (6nt barcode + constant G at the ligation site), the samples were re-pooled into a single tube. The nascet RNA was selected with streptavidin beads (x3 during the PRO-IP-seq protocol). The 5'-ends of nascent transcripts were decapped, repaired and ligated to UMI-containing adapters (6-nt UMI + constant C at the ligation site). The nascent RNA was reverse-transcribed, quality controlled and amplified to final sequencing library (Illumina TruSeq small RNA).
Illumina NextSeq 500 and Illumina NovaSeq6000

tag: protocol

value: Heat treated at 42degreeC for 30 minutes (HS30)

value: no antibody

tag: antibody epitope

tag: library preparation

value: PRO-IP-seq


title: mm_islets_dbhet_RNAseq_B

value: db/+ age-matched control for db/db Rep 2


title: mm_islets_dbhet_RNAseq_C

value: db/+ age-matched control for db/db Rep 3


title: i3_HS30_S7_rep3

description:
nascent RNA
iPRO_HS30_S7_BRs_normalized_pl.bigWig
iPRO_HS30_S7_BRs_normalized_mn.bigWig

value: Millipore 04-1570

value: serine-7-phosphorylated CTD (ser7PhCTD)


title: i3_HS30_S5_rep3

description:
nascent RNA
iPRO_HS30_S5_BRs_normalized_pl.bigWig
iPRO_HS30_S5_BRs_normalized_mn.bigWig

value: serine-5-phosphorylated CTD (ser5PhCTD)


title: Brain [10]

value: CON


title: mm_islets_dbhet_RNAseq_A

value: db/+ age-matched control for db/db Rep 1


title: i3_HS30_S2_rep3

description:
nascent RNA
iPRO_HS30_S2_BRs_normalized_pl.bigWig
iPRO_HS30_S2_BRs_normalized_mn.bigWig

value: serine-2-phosphorylated CTD (ser2PhCTD)


title: i3_HS30_CTD_rep3

description:
nascent RNA
iPRO_HS30_CTD_BRs_normalized_pl.bigWig
iPRO_HS30_CTD_BRs_normalized_mn.bigWig

value: AbCam YWG16

value: unphosphorylated CTD (unPhCTD)


title: mm_islets_LsdKOD21_RNAseq_E

value: Wk3 Lsd1 KO Rep 5


title: Brain [9]

value: RES


title: i3_NHS_input_rep3

description:
nascent RNA
iPRO_NHS_input_BRs_normalized_pl.bigWig
iPRO_NHS_input_BRs_normalized_mn.bigWig

value: No heat shock, maintained at 37degreeC (NHS)


title: Brain [8]

value: SUS


title: i3_NHS_S7_rep3

description:
nascent RNA
iPRO_NHS_S7_BRs_normalized_pl.bigWig
iPRO_NHS_S7_BRs_normalized_mn.bigWig


title: mm_islets_dbdb_RNAseq_B

value: db/db recently hyperglycemic (250 mg/dL) Rep 2


title: mm_islets_LsdKOD21_RNAseq_D

value: Wk3 Lsd1 KO Rep 4


title: Brain [7]


title: i3_NHS_S2_rep3

description:
nascent RNA
iPRO_NHS_S2_BRs_normalized_pl.bigWig
iPRO_NHS_S2_BRs_normalized_mn.bigWig

value: PRO-IP-seq


title: i3_NHS_S5_rep3

description:
nascent RNA
iPRO_NHS_S5_BRs_normalized_pl.bigWig
iPRO_NHS_S5_BRs_normalized_mn.bigWig


title: Brain [6]


title: i3_NHS_CTD_rep3

description:
nascent RNA
iPRO_NHS_CTD_BRs_normalized_pl.bigWig
iPRO_NHS_CTD_BRs_normalized_mn.bigWig


title: mm_islets_LsdKOD21_RNAseq_C

value: Wk3 Lsd1 KO Rep 3


title: RNAseq_GRHL2_OE_NO_DOX_H9_d7_rep2

data_processing:
Tophat used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Genome_build: hg38
Supplementary_files_format_and_content: text file, raw counts

source_name: H9 no Dox

extract_protocol:
Cells were lysed in Trizol (Invitrogen), and the aqueous layer was isolated as indicated by the manufacturer. RNA was purified with a RNeasy kit (Qiagen). DNase (Qiagen) treatment was added to the column prior to elution as per manufacturer instructions.
RNA-seq libraries were prepared using the KAPA kit for PolyA enriched mRNA-seq (Roche) according to the manufacturer’s protocol. Libraries were pooled and sequenced on a NovaSeq. Two independent, biological replicates were sequenced per cell type.

value: No Treatment


title: mm_islets_LsdKOD21_RNAseq_B

value: Wk3 Lsd1 KO Rep 2


title: Brain [5]


title: RNAseq_GRHL2_OE_NO_DOX_H9_d7_rep1


title: mm_islets_LsdCtrlD21_RNAseq_C

value: Control for Wk3 Lsd1 KO Rep 3


title: Brain [3]


title: Brain [4]


title: mm_islets_LsdCtrlD21_RNAseq_B

value: Control for Wk3 Lsd1 KO Rep 2


title: RNAseq_GRHL2_KO_H9_D7_rep1

source_name: H9 day7

value: 7 days RA/BMP4


title: RNAseq_GRHL2_OE_DOX_H9_d7_rep1

source_name: H9 Dox

value: 7 days doxycycline to induce GRHL2 overexpression


title: RNAseq_GRHL2_KO_H9_D7_rep2


title: scRNA_day7_GRHL2_KO

description: single cell RNA-seq

data_processing:
FASTQ files were processed using 10x Genomics Cell Ranger Arc 2.0.0 and the human reference genome hg38.
Seurat was used for QC and to call clusters
Monocle was used for pseudotime analysis
Genome_build: hg38
Supplementary_files_format_and_content: h5, tsv

extract_protocol:
Single cell suspensions were prepared with Accutase, and cells were frozen in BamBanker (Wako Chemicals). Cells were thawed in cryovials in a 37°C water bath for 1-2 min, spun out of freezing media, and any large clumps were removed with 40μM Flowmi Cell Strainers. Dead cells were eliminated with a dead cell removal kit (Miltenyi) per manufacturer instructions.
1 million cells per sample were lysed for 5 min in 1X chilled lysis buffer (10mN Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute, 0.01% digitonin, 1% BSA, 1mM DTT, and 1U/μL RNase inhibitor). Cells were washed 3 times with chilled wash buffer (10mN Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20, 1mM DTT, and 1U/μL RNase inhibitor) and resuspended at a concentration of 2,700 nuclei/μL in Diluted Nuclei Buffer (1X Nuclei Buffer (10x Genomics), 1mM DTT, 1U/μL RNase Inhibitor). 6,000 nuclei were targeted for multiome library prep per the manufacturer’s instructions (10x Genomics Multiome ATAC + Gene Expression User Guide CG000338). scATAC libraries were sequenced on a NovaSeq SP100 lane at a depth of 25,000 read pairs per nucleus. scRNA libraries were sequenced on an S4 NovaSeq at a depth of 20,000 read pairs per nucleus.
10x multiome (scRNA+scATAC)

value: GRHL2 KO


title: Brain [2]


title: scATAC_day7_GRHL2_KO

description: single cell ATAC


title: scRNA_day7_WT

description: single cell RNA-seq

value: WT


title: mm_islets_LsdCtrlD21_RNAseq_A

value: Control for Wk3 Lsd1 KO Rep 1


title: Brain [1]

value: CON


title: scATAC_day7_WT

description: single cell ATAC


title: GBM_VU66

description:
tissues_anticodon_RPM_full-length_tRNA.csv
tissues_anticodon_RPM_all_tRNA.csv

data_processing:
Raw Illumina reads were first pre-processed using sRNAbench (Aparicio-Puerta et al., NAR, 2019; Aparicio-Puerta et al., NAR, 2022) for adapter removal and quality control.
The standard sRNAbench mapping step using bowtie was extended with a second round of Smith–Waterman alignment implemented using BioJava BioJava to recover additional tRNA-derived reads by further allowing gaps and/or mismatches.
Reference libraries were obtained from GtRNAdb 2.0 (Homo sapiens, GRCh38/hg38) for nuclear tRNAs and mitotRNAdb for mitochondrial tRNAs.
TRNA expression was profiled at different levels: tRNA gene level, anticodon level and per amino acid. Reads containing the 5’ end of the sequence with complete/partial or no CCA ending were classified as mature full-length transcripts.
Genome_build: hg38; gtRNAdb Release 18
Supplementary_files_format_and_content: The cell lines used in this study have processed tRNA read length files in csv format. Anticodon read counts for full-length tRNA and tsRNA  in .csv format are provided for all tissues used in this study.

extract_protocol:
Total RNA was extracted from various tissue samples and SU-DHL-5, SNB-75, HEK293T and hESC cell lines, using mirVana Isolation Kit. For all samples, on-column RNAse-free DNase treatment was performed. Deacylation was then performed by incubating total RNA in 0.1 M Tris-HCL pH 9.0 and 1 mM EDTA for 30 minutes at 37 °C. Demethylation reaction was performed on total RNA. Briefly, 2 ug total RNA was treated with 19 uM of AlkB consisting of 8.5uM AlkB WT and 10.5 uM AlkB-D135S mutant, 10 mM KCl, 2 mM MgCl2, 283 uM freshly prepared (NH4)2Fe(SO4)2 6H2O, 0,3 mM 2-ketoglutarate, 2 mM freshly made L-ascorbic acid, 40U RNase Inhibitor and 50 mM MES buffer pH 5.0 in a total volume of 40 ul. Reactions were incubated at 25°C for 2h and quenched with 5 mM EDTA. RNA was recovered by an Oligo Clean&Concentrator-5 kit and eluted in 6 ul Nuclease-free water.
Native total RNA or demethylated total RNA was used for each cell line and tissue sample. Sequencing libraries were generated using ALL-tRNAseq library preparation. For the workflow of ALL-tRNAseq a 5’ phosphorylated 3’ end adapter with 4 randomized nucleotides at the 5’ end and a 3’ blocking group (3C Spacer; 3SpC3, IDT) was adenylated by Mth RNA ligase and then ligated to the RNA template using a T4 RNA ligase 2, truncated KQ for 1 h at 25°C in the presence of 20% PEG. Ligated RNA was gel-purified and size-fractionated on a Novex TBE-urea 10% denaturing polyacrylamide gel to enrich small RNA molecules using two FAM-markers of 25 nt and 39 nt and an upper marker of the low range ssRNA ladder at 150 nt. Gels were stained using 1x SYBR gold nucleic acid stain in 1x TBE for 10 minutes and 3’adapter-ligated-RNA in size range of 39-150 nt were excised on a blue light transilluminator. RNA was recovered from excised polyacrylamide gel pieces by crushing the gel fragments and soaking them in 0.3M NaCl overnight at 4°C and subsequent ethanol precipitation, 5’ adapters with 4 terminal, randomized nucleotides at 3’ end were added, using T4 RNA ligase and ATP. Ligation was performed for 1h at 25°C in the presence of 20% PEG. Thereafter, reverse transcription was performed for 1h at 50°C or 42°C using SuperScript III or MarathonRT, respectively. Reactions were terminated by incubation with 0,25 M NaOH, at 95°C for 3 min, then neutralized with 0,25 M HCl. Next, cDNA was purified using MinElute Reaction Cleanup kit and PCR amplified using Phusion high-fidelity PCR master mix for 12 cycles of 98°C for 5 s, 62°C for 10s and 72°C for 10 s. A 6-nt index sequences was introduced into the adapter sequence to enable library identification from a sequenced pool. PCR products were equimolarly pooled for cluster generation without additional size-selection. Sequencing of the ALL-tRNAseq libraries was performed as single-end reads for 150 cycles on NovaSeq 6000.

value: glioblastoma (GBM)

value: demethylation


title: GBM_VU50


title: mm_islets_LsdKOD7_RNAseq_B

value: Wk1 Lsd1 KO Rep 2


title: GBM_VU76


title: Pep30, HEK293T BAG6 KO, low mCherry-to-EGFP ratio

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

data_processing:
Reads were aligned to a custom index for the Pep30 library generated with the command bowtie-build in bowtie version 1.2.3 and the option -v 3 --best (best alignment with up to 3 mismatches). The counts of each Pep30 sequence were extracted from the alignment with the bash command cut -f 3 | sort | uniq -c.
Assembly: Custom
Supplementary files format and content: Pep30lib-GFP-high-vs-low.txt: tab-delimited. Columns are: ID, DNA sequence, GFP_high read count, GFP_low read count, Peptide
Supplementary files format and content: Pep30lib-GFP-mCherry-ratio.txt: space-delimited. Columns are: ID Seq Peptide KO_high KO_midhigh KO_midlow KO_low WT_high WT_midhigh WT_midlow WT_low

growth_protocol: HEK293T cells used in this study were purchased from ATCC, from which the BAG6 KO cells were derived using CRISPR/Cas9. Cells were cultured in DMEM with 4.5 g/L D-Glucose supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin was added except when producing lentivirus. Low passage number cells were used and maintained under 90% visual confluency. Cells were maintained at 5% CO2 and 37 °C. HEK293T cells used in this study were confirmed to be negative for Mycoplasma Contamination and routinely tested using the MycoAlertTM Mycoplasma Detection Kit (Lonza, LT07-418).

extract_protocol:
Genomic DNA was isolated from the cell populations using QIAGEN QIAamp DNA mini kit or Machery Nagel Nucleospin Tissue kit
genomic DNA was eluted in 50 uL of elution buffer. Libraries were then amplified using PCR with custom Illumina adapters, using Q5 high-fidelity PCR mix with 1000 ng input gDNA per sample. Libraries were amplified for a total of 24-27 cycles. After amplification, libraries were cleanup up using SPRISelect beads at a ratio of 0.7x. Purified library size was confirmed via gel and libraries were quantified using the KAPA qPCR Illumina library quantification kit. Libraries were subsequently pooled in a ratio based on the number of total cells collected from each sample.
DNA amplicon sequencing

treatment_protocol: Sorting based on EGFP alone in HEK293T cells: cells were transduced with Pep30 lentivirus at low MOI, grown for 6 days, then FACS sort top and bottom 20% GFP cells. Sorting based on mCherry/EGFP ratio of WT and BAG6 KO cells: HEK293T as well as a clonal BAG6 knockout cell line were reverse transduced with the Pep30 library such that less than 30% of cells were transduced (thus are most likely a single integration per cell). The virus-containing media was removed after 24 hours and fresh media with 10% FBS and 1% PenStrep was added to the plates. After another 24 hours, transduced cells were purified based on their expression of mCherry. The transduced populations were returned to culture and allowed to grow out for an additional 6 days, with passaging as necessary to maintain confluence below 80%. After 6 days, both populations were sorted into 4 bins based on the ratio of EGFP/mCherry expression (High, mid-high, mid-low, and low) using a FACSAria cell sorter. The same mCherry/EGFP ratio gates were used for both WT and BAG6 KO cells. Sorted cells were spun down at 500 RCF for 5 minutes, washed once with 1000 uL PBS, spun down again, then frozen at -20 as a cell pellet.

value: Human embryonic kidney

value: BAG6 KO


title: Pep30, HEK293T BAG6 KO, mid-low mCherry-to-EGFP ratio


title: GBM_VU34


title: GBM_VU32


title: mm_islets_LsdKOD21_RNAseq_A

value: Wk3 Lsd1 KO Rep 1


title: GBM_VU30


title: RNAseq_GRHL2_OE_DOX_H9_d7_rep2


title: mm_islets_LsdCtrlD7_RNAseq_C

value: Control for Wk1 Lsd1 KO Rep 3


title: GBM_VU21


title: mm_islets_LsdKOD7_RNAseq_A

value: Wk1 Lsd1 KO Rep 1


title: mm_islets_LsdCtrlD7_RNAseq_B

value: Control for Wk1 Lsd1 KO Rep 2


title: Pep30, HEK293T BAG6 KO, high mCherry-to-EGFP ratio


title: Pep30, HEK293T WT, low mCherry-to-EGFP ratio

value: wild-type


title: mm_islets_LsdCtrlD7_RNAseq_A

value: Control for Wk1 Lsd1 KO Rep 1


title: Pep30, HEK293T WT, mid-low mCherry-to-EGFP ratio


title: mm_islets_LsdKOD7_RNAseq_C

value: Wk1 Lsd1 KO Rep 3


title: GBM_VU11


title: GBM_VU07


title: HB4

source_name: hystologically normal brain

value: brain


title: mm_islets_10pmFast_RNAseq_C

value: Fasted (16h) Rep 3


title: HB3


title: GBM_VU09


title: DLBCL_HEM46

value: primary Diffuse Large B-cell Lymphoma (DLBCL)


title: HB1


title: Pep30, HEK293T WT, high mCherry-to-EGFP ratio


title: mm_islets_10pmFast_RNAseq_A

value: Fasted (16h) Rep 1


title: Pep30, HEK293T WT, mid-high mCherry-to-EGFP ratio


title: mm_islets_10pmFast_RNAseq_B

value: Fasted (16h) Rep 2


title: Pep30, HEK293T BAG6 KO, mid-high mCherry-to-EGFP ratio


title: DLBCL_HEM35


title: DLBCL_HEM36


title: DLBCL_HEM25


title: GBM_VU18

value: glioblastoma (GBM)


title: DLBCL_HEM37

value: demethylation


title: GBM_VU17


title: DLBCL_HEM24


title: mm_islets_10pmFed_RNAseq_B

value: Fed (4h) Rep 2


title: DLBCL_HEM21


title: DLBCL_HEM06


title: mm_islets_10pmFed_RNAseq_A

value: Fed (4h) Rep 1


title: Tissue-Epithelial Ovarian Cancer-Sample7-Rep1

city: Istanbul

first: Tuba

last: Gunel

state: Fatih

address: Balabanaga mahallesi sehzadebasi cad.

country: Turkey

institute: Istanbul University

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 7
Tissue sample, Epithelial Ovarian Cancer, Sample7, Replicate 1

hyb_protocol: The labelled miRNAs were hybridized for 24 h on “Human miRNA Microarray Version 16” (Agilent Technologies, Santa Clara, CA, USA) slides. Labelled miRNAs were blocked by “10X GE Blocking agent” and were washed using Gene Expression Wash Buffer 1 and 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (Model G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing: The images provided after scanning were analyzed by “Agilent Feature Extraction (v.11.0.1.1)” software using default parameters (protocol miRNA_1100_Jul11 and Grid: 070156_D_F_20141006).

label_protocol: For labelling, miRNA Labelling and Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA) was used according to the manufacturer's instructions. Total RNAs extracted from both serum and tissue were labelled by cyanine 3-cytidine bisphosphate (pCp-Cy3).

growth_protocol: About 500 mg of tissue samples were taken in sterile centrifuge tubes containing RNAlater Solution (Ambion, Life Technology, USA) stabilization and storage solution, stored at +4°C overnight and then stored at -80°C until studied. Peripheral blood was collected into EDTA tubes (5 ml).

extract_protocol: Total RNA was isolated with “QIAGEN RNeasy Plus Mini Kit” (QIAGEN, Germany) from tissue samples. The quantity of obtained total RNA was measured by NanoDrop IMPLEN P-Class (Thermo Fisher Scientific, Waltham, MA, USA), and the quality controls of them were done by Agilent RNA 6000 Nano Kit on Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). After RNA extracts were evaluated with bioanalyzer, 8 samples with the highest quality (RNA Integrity Number (RIN) value >5) according to RIN were selected for microarray study. To extract total RNA including miRNA from serum (500ul input), “mirVana™ PARIS™ RNA and Native Protein Purification Kit” (Ambion, Life Technology, USA) was used following the manufacturer’s protocol. The purity and concentration of RNA samples of serum were determined by NanoDrop IMPLEN P-Class (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: Tissues are digested with liquid nitrogen before isolation of total RNA from tissue samples. Crushed samples (30-60 mg is preferred) are placed in 2 ml microcentrifuge tubes. Blood samples were immediately centrifuged at 3500xg for 15 min at 4°C. The supernatant serum was transferred to RNase-free tubes after centrifugation. Sample serum fractions were collected and stored at -80°C until laboratory workup.

tag: tissue

value: EOC tissue


title: DLBCL_HEM14


title: DLBCL_HEM05


title: Obese+sGCstim 3

city: Berlin

middle: S

last: Balzer

address: Charitéplatz 1

department: Dpt. of Nephrology and Medical Intensive Care

institute: Charité - Universitätsmedizin Berlin

description:
EXPORT_GEO_meta.data.csv.gz
EXPORT_GEO_counts_postfilter.rds.gz

data_processing:
Raw fastq files were aligned and quantified with CellRanger v6 using a custom pre-mRNA GTF built from the ENSEMBL rn6 genome to include intronic regions.     Seurat was used for data quality control, preprocessing, and dimensional reduction. In short, for every sample, a separate gene-cell data matrix was generated and poor-quality cells with <200 or >3,000 expressed genes and mitochondrial gene percentages >15 were excluded. Remaining barcodes of high-quality nuclei were log-normalized and the top 3,000 highly variable genes were identified with the vst method. After data scaling, linear dimension reduction was performed using principal component analysis (PCA). A shared nearest neighbor network was created based on Euclidian distances between cells in multidimensional PC space using the first 15 dimensions before clustering using FindClusters and dimension reduction using RunUMAP functions, respectively.
Doublet-like cells were identified using DoubletFinder(McGinnis et al., 2019). Assuming no ground truth to facilitate an unbiased approach, pK was identified using paramSweep_v3 function with PCs=1:15. Homotypic doublet proportion was estimated with function modelHomotypic using above clustering information. Finally, function doubletFinder_v3 was run with pN=0.25, pK and nExp as identified by the functions above and Uniform Manifold Approximation and Projections (UMAPs) were manually inspected for singlet/doublet status.
After determining high quality ambient RNA-corrected singlet barcodes for every sample individually, 10X filtered output matrices of all 12 samples were again corrected for ambient RNA and subset to singlet barcodes, as determined above, before merging of Seurat objects. The Seurat preprocessing pipeline was then rerun on the merged object (normalization, identification of highly variable genes, scaling, linear dimension reduction), regressing out nCount_RNA during scaling. Then, Harmony(Korsunsky et al., 2019) was used to correct for potential batch effects. The first 30 Harmony-corrected principal components were used for nearest neighbor network creation, clustering, and dimension reduction. A clustering resolution of 0.9 was chosen to best reflect separate cell identities without artificial over-clustering.
Assembly: rn6
Supplementary files format and content: Counts matrix RDS object
Supplementary files format and content: metadata CSV table

molecule: polyA RNA

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Kidneys were harvested, cut into quarters, snap frozen and stored at -80 °C for further analysis. Nuclei were isolated using lysis buffer containing 50% ST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2 in ultrapure water), 2% Nonidet P40 Substitute, 0.2% ultrapure BSA (50 mg/mL, AM2616, Thermofisher Scietific) and 1% Protector RNase inhibitor (3335399001, Sigma Aldrich). 10-30 mg of frozen kidney tissue was minced with a razor blade into 1-2 mm pieces in 1 mL of lysis buffer. Then, chopped tissue was transferred to a dounce homogenizer. After adding 1 mL of lysis buffer tissue was homogenized using pestle A and B (10 times each). The homogenized tissue was filtered through a 40 µm strainer (08-771-1, Fisher Scientific) and the strainer was washed with 2 mL wash buffer (containing 50% ST buffer, 0.2% ultrapure BSA 50 mg/mL, and 1% protector RNase inhibitor). The washed content was centrifuged at 500 g for 5 minutes at 4 °C. Next, the pellet was resuspended in wash buffer, filtered through a 40 µm Flowmi cell strainer (BAH136800040-50EA, Sigma Aldrich). Intact nuclei shape was confirmed under a microscope, and nuclei were counted.
10,000 nuclei were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, PN-1000121). The cDNA and library was made using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262) according to the manufacturer’s protocol. Quality control for the libraries was performed using Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Libraries were sequenced on an Illumina Novaseq 6000 system with 2 × 150 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index and 91 bp Read2 for transcript.

treatment_protocol: Male ZSF1 lean and ZSF1 obese rats (ZSF1-LeprfaLeprcp/Crl) were obtained from Charles River Laboratories Inc. (251 Ballardvale St, Wilmington, Massachusetts). The animals were housed in a temperature- (22±2°C) and humidity-controlled environment with a 12h light/dark cycle. Access to water and high energy rodent chow Purina 5008 was provided ad libitum. The study was conducted at the Wuppertal Research Center of Bayer AG. The protocol was approved by the institutional animal care and use committee of Bayer AG and was in compliance with the guidelines of the local animal welfare authorities for the German state of North‐Rhine Westphalia (Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV) Nordrhein‐Westfalen; N0400a022). At the age of 13-14 weeks, ZSF1 obese rats were randomly assigned to a 12-week daily treatment with vehicle (10% ethanol, 40% Kolliphor® HS15, and 50% water), 3 mg/kg BID sGCact = BAY 1101042 = Runcaciguat, or 3 mg/kg QD sGCstim = BAY 1165747); n=10 each. ZSF1 lean rats (n=6) were not treated and served as controls.

value: kidney

tag: phenotype

value: obese


title: Tissue-Epithelial Ovarian Cancer-Sample6-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 6
Tissue sample, Epithelial Ovarian Cancer, Sample6, Replicate 1


title: HLN3

source_name: reactive lymph node

value: lymph node

tag: treatment


title: HLN2


title: HLN1


title: mm_islets_10pmFed_RNAseq_C

tag: chip antibody

value: Fed (4h) Rep 3


title: Tissue-Epithelial Ovarian Cancer-Sample5-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 5
Tissue sample, Epithelial Ovarian Cancer, Sample5, Replicate 1


title: Obese+sGCstim 1

tag: genotype


title: hESC T5 ALL-tRNAseq_2

data_processing:
Raw Illumina reads were first pre-processed using sRNAbench (Aparicio-Puerta et al., NAR, 2019; Aparicio-Puerta et al., NAR, 2022) for adapter removal and quality control.
The standard sRNAbench mapping step using bowtie was extended with a second round of Smith–Waterman alignment implemented using BioJava BioJava to recover additional tRNA-derived reads by further allowing gaps and/or mismatches.
Reference libraries were obtained from GtRNAdb 2.0 (Homo sapiens, GRCh38/hg38) for nuclear tRNAs and mitotRNAdb for mitochondrial tRNAs.
TRNA expression was profiled at different levels: tRNA gene level, anticodon level and per amino acid.
Genome_build: hg38; gtRNAdb Release 18
Supplementary_files_format_and_content: The cell lines used in this study have processed tRNA read length files in csv format. Anticodon read counts for full-length tRNA and tsRNA  in .csv format are provided for all tissues used in this study.

source_name: human embryonic stem cells after ATRA-induced differentiation

growth_protocol: hESC cell line WA09 from WiCell was maintained in complete TESR-E8 medium supplemented with 1% penicillin/streptomycin on Vitronectin XF™ coated plates. Passaging was performed with Gentle Cell Dissociation Reagent. Media was supplemented with 10 µM ROCK inhibitor after passaging.

extract_protocol:
Total RNA was extracted from various tissue samples and SU-DHL-5, SNB-75, HEK293T and hESC cell lines, using mirVana Isolation Kit. For all samples, on-column RNAse-free DNase treatment was performed. De-aminoacylation was then performed by incubating total RNA in 0.1 M Tris-HCL pH 9.0 and 1 mM EDTA for 30 minutes at 37 °C. Demethylation reaction was adapted from a previously published method (Hrabeta-Robinson et al, Methods in Mol Biol, 2017) and performed on total RNA. Briefly, 2 ug total RNA was treated with 19 uM of AlkB consisting of 8.5uM AlkB WT and 10.5 uM AlkB-D135S mutant, 10 mM KCl, 2 mM MgCl2, 283 uM freshly prepared (NH4)2Fe(SO4)2 6H2O, 0,3 mM 2-ketoglutarate, 2 mM freshly made L-ascorbic acid, 40U RNase Inhibitor and 50 mM MES buffer pH 5.0 in a total volume of 40 ul. Reactions were incubated at 25°C for 2h and quenched with 5 mM EDTA. RNA was recovered by an Oligo Clean&Concentrator-5 kit and eluted in 6 ul Nuclease-free water.
Native total RNA or demethylated total RNA was used for each cell line and tissue sample. Sequencing libraries were generated using ALL-tRNAseq library preparation. For the workflow of ALL-tRNAseq a 5’ phosphorylated 3’ end adapter with 4 randomized nucleotides at the 5’ end and a 3’ blocking group (3C Spacer; 3SpC3, IDT) was adenylated by Mth RNA ligase and then ligated to the RNA template using a T4 RNA ligase 2, truncated KQ for 1 h at 25°C in the presence of 20% PEG. Ligated RNA was gel-purified and size-fractionated on a Novex TBE-urea 10% denaturing polyacrylamide gel to enrich small RNA molecules using two FAM-markers of 25 nt and 39 nt and an upper marker of the low range ssRNA ladder at 150 nt. Gels were stained using 1x SYBR gold nucleic acid stain in 1x TBE for 10 minutes and 3’adapter-ligated-RNA in size range of 39-150 nt were excised on a blue light transilluminator. RNA was recovered from excised polyacrylamide gel pieces by crushing the gel fragments and soaking them in 0.3M NaCl overnight at 4°C and subsequent ethanol precipitation, 5’ adapters with 4 terminal, randomized nucleotides at 3’ end were added, using T4 RNA ligase and ATP. Ligation was performed for 1h at 25°C in the presence of 20% PEG. Thereafter, reverse transcription was performed for 1h at 50°C or 42°C using SuperScript III or MarathonRT, respectively. Reactions were terminated by incubation with 0,25 M NaOH, at 95°C for 3 min, then neutralized with 0,25 M HCl. Next, cDNA was purified using MinElute Reaction Cleanup kit and PCR amplified using Phusion high-fidelity PCR master mix for 12 cycles of 98°C for 5 s, 62°C for 10s and 72°C for 10 s. A 6-nt index sequences was introduced into the adapter sequence to enable library identification from a sequenced pool. PCR products were equimolarly pooled for cluster generation without additional size-selection. Sequencing of the ALL-tRNAseq libraries was performed as single-end reads for 150 cycles on NovaSeq 6000.

treatment_protocol: For the differentiation assay hESCs were exposed to all-trans retinoic acid at a final concentration of 1 µM in plain TESR-E8 medium supplemented with 1% Penicillin/streptomycin. Medium was changed daily. Cells were harvested after 0 (no ATRA), 1, 3, and 5 days after ATRA induction.

tag: cell line

value: human embryonic stem cells


title: hESC T5 ALL-tRNAseq_3


title: hESC T5 ALL-tRNAseq_1


title: Obese+sGCstim 2


title: Tissue-Epithelial Ovarian Cancer-Sample4-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 4
Tissue sample, Epithelial Ovarian Cancer, Sample4, Replicate 1

tag: age


title: Tissue-Epithelial Ovarian Cancer-Sample8-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 8
Tissue sample, Epithelial Ovarian Cancer, Sample8, Replicate 1


title: hESC T0 ALL-tRNAseq_2

source_name: human embryonic stem cells


title: hESC T0 ALL-tRNAseq_1


title: Obese+sGCact 2


title: Obese+sGCact 3


title: Tissue-Epithelial Ovarian Cancer-Sample3-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 3
Tissue sample, Epithelial Ovarian Cancer, Sample3, Replicate 1


title: hESC T0 ALL-tRNAseq_3


title: HEK293T ALL-tRNAseq_3

source_name: HEK293T cells

growth_protocol: HEK293T was cultured at 37°C in a humidified atmosphere containing 5% CO2 in complete Dulbecco’s Modified Eagle Medium. Medium was supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

value: HEK293T cells


title: Tissue-Epithelial Ovarian Cancer-Sample2-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 2
Tissue sample, Epithelial Ovarian Cancer, Sample2, Replicate 1


title: Tissue-Epithelial Ovarian Cancer-Sample1-Rep1

description:
MiRNA expressions in epithelial ovarian cancer tissue samples of sample 1
Tissue sample, Epithelial Ovarian Cancer, Sample1, Replicate 1


title: HEK293T ALL-tRNAseq_1


title: Obese+sGCact 1


title: HEK293T ALL-tRNAseq_2


title: SNB-75_mRT-buffer-treated_2

source_name: SNB-75 cells

growth_protocol: SNB-75 was cultured at 37°C in a humidified atmosphere containing 5% CO2 in complete Dulbecco’s Modified Eagle Medium. Medium was supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from various tissue samples and SU-DHL-5, SNB-75, HEK293T and hESC cell lines, using mirVana Isolation Kit. For all samples, on-column RNAse-free DNase treatment was performed. Deacylation was then performed by incubating total RNA in 0.1 M Tris-HCL pH 9.0 and 1 mM EDTA for 30 minutes at 37 °C. Demethylation reaction was performed on total RNA. Briefly, 2 ug total RNA was treated with 19 uM of AlkB consisting of 8.5uM AlkB WT and 10.5 uM AlkB-D135S mutant, 10 mM KCl, 2 mM MgCl2, 283 uM freshly prepared (NH4)2Fe(SO4)2 6H2O, 0,3 mM 2-ketoglutarate, 2 mM freshly made L-ascorbic acid, 40U RNase Inhibitor and 50 mM MES buffer pH 5.0 in a total volume of 40 ul. Reactions were incubated at 25°C for 2h and quenched with 5 mM EDTA. RNA was recovered by an Oligo Clean&Concentrator-5 kit and eluted in 6 ul Nuclease-free water.
Native total RNA or demethylated total RNA was used for each cell line and tissue sample. Sequencing libraries were generated using NEBNext Multiplex small RNA library preparation set for Illumina, according to manufacturer’s instructions, or ALL-tRNAseq. For the workflow of ALL-tRNAseq a 5’ phosphorylated 3’ end adapter with 4 randomized nucleotides at the 5’ end and a 3’ blocking group (3C Spacer; 3SpC3, IDT) was adenylated by Mth RNA ligase and then ligated to the RNA template using a T4 RNA ligase 2, truncated KQ for 1 h at 25°C in the presence of 20% PEG. Ligated RNA was gel-purified and size-fractionated on a Novex TBE-urea 10% denaturing polyacrylamide gel to enrich small RNA molecules using two FAM-markers of 25 nt and 39 nt and an upper marker of the low range ssRNA ladder at 150 nt. Gels were stained using 1x SYBR gold nucleic acid stain in 1x TBE for 10 minutes and 3’adapter-ligated-RNA in size range of 39-150 nt were excised on a blue light transilluminator. RNA was recovered from excised polyacrylamide gel pieces by crushing the gel fragments and soaking them in 0.3M NaCl overnight at 4°C and subsequent ethanol precipitation, 5’ adapters with 4 terminal, randomized nucleotides at 3’ end were added, using T4 RNA ligase and ATP. Ligation was performed for 1h at 25°C in the presence of 20% PEG. Thereafter, reverse transcription was performed for 1h at 50°C or 42°C using SuperScript III or MarathonRT, respectively. Reactions were terminated by incubation with 0,25 M NaOH, at 95°C for 3 min, then neutralized with 0,25 M HCl. Next, cDNA was purified using MinElute Reaction Cleanup kit and PCR amplified using Phusion high-fidelity PCR master mix for 12 cycles of 98°C for 5 s, 62°C for 10s and 72°C for 10 s. A 6-nt index sequences was introduced into the adapter sequence to enable library identification from a sequenced pool. PCR products were equimolarly pooled for cluster generation without additional size-selection. Sequencing of the NEBNext small RNA libraries was performed as single-end reads using the Illumina Miseq V2 platform and ALL-tRNAseq was performed as single-end reads for 150 cycles on NovaSeq 6000.

value: buffer-treated

value: SNB-75 cells


title: Tissue-Simple Ovarian Cyst-Control7-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 7
Tissue sample, Simple Ovarian Cyst, Control7, Replicate 1

value: benign ovarian neoplastic tissue


title: SNB-75_mRT-buffer-treated_1


title: SNB-75_mRT-untreated

value: untreated


title: Obese 3

value: vehicle


title: SNB75 ALL-tRNAseq_2


title: Obese 2


title: Tissue-Simple Ovarian Cyst-Control6-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 6
Tissue sample, Simple Ovarian Cyst, Control6, Replicate 1


title: Obese 1


title: SNB75 ALL-tRNAseq_1


title: Lean 3

value: lean


title: Tissue-Simple Ovarian Cyst-Control5-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 5
Tissue sample, Simple Ovarian Cyst, Control5, Replicate 1


title: SU-DHL-5 ALL-tRNAseq_1

value: SU-DHL-5 cells


title: SNB-75_SSIII-DM-treated_1

value: demethylation


title: Lean 2


title: Tissue-Simple Ovarian Cyst-Control8-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 8
Tissue sample, Simple Ovarian Cyst, Control8, Replicate 1


title: Lean 1


title: high target, g3, no spike in [XP013]

address: 630 West 168th Street

department: Medicine/Systems Biology

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: kallisto counts and tpm file (txt)

source_name: HEK293T_high target_g3_no spike in

growth_protocol: HEK293T cells were cultured with DMEM and 10% FBS

extract_protocol:
Total RNA were extracted using Trizol
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry. Libraries are then sequenced using Illumina NovaSeq 6000. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: Transfection in HEK293T cells was with Lipofectamine 3000 following the manufacture’s protocol. All samples were transfected with RfxCas13d (CasRx with NLS), target reporter (DsRed), control reporter (BFP), and gRNA (g3: targeting, g11: control). Unless noted, all samples were mixed with 10% mouse MEF cells prior to total RNA extraction

tag: sample group

value: high target_g3_no spike in


title: high target, g3, no spike in [XP014]


title: low target, g11, rep 3 [XP012]

source_name: HEK293T_low target_g11

value: low target_g11


title: low target, g11, rep 2 [XP011]


title: low target, g11, rep 1 [XP010]


title: low target, g3, rep 3 [XP009]

source_name: HEK293T_low target_g3

value: low target_g3


title: Tissue-Simple Ovarian Cyst-Control4-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 4
Tissue sample, Simple Ovarian Cyst, Control4, Replicate 1


title: Tissue-Simple Ovarian Cyst-Control2-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 2
Tissue sample, Simple Ovarian Cyst, Control2, Replicate 1


title: Tissue-Simple Ovarian Cyst-Control3-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 3
Tissue sample, Simple Ovarian Cyst, Control3, Replicate 1


title: Tissue-Simple Ovarian Cyst-Control1-Rep1

description:
MiRNA expressions in simple ovarian cyst tissue samples of control 1
Tissue sample, Simple Ovarian Cyst, Control1, Replicate 1


title: mutation-1

city: Tianjin

first: Wange

last: Lu

address: 94 Weijin Road

institute: Nankai University

data_processing:
Clean reads were mapped to the Ensemble hg19 human genome using Hisat2 with default parameters.
Gene reads were counted by Htseq. Fold changes (FC) were computed as a log2 ratio of normalized reads per gene using the DEseq2 R package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Prostate

growth_protocol: 22Rv1 cell lines were obtained from ATCC. Cells were incubated at 37 ℃ in 5% CO2 and cultured in complete RPMI1640 (Gibco) supplemented with 10% FBS (Bio-logical Industries) and 1% Penicillin/Streptomycin (Gibco).

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent (ThermoFisher Scientific, 15596018) based on the manufacturer’s protocol. 2 μg RNA was reverse transcribed to cDNA using the PrimeScript RT reagent with a gDNA eraser Kit (Takara, no. RRO47B).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

tag: genotype/variation

value: :G->A mutation (rs10486567, homozygous to homozygous


title: low target, g3, rep 2 [XP008]


title: mutation-2


title: low target, g3, rep 1 [XP007]


title: TFAP2A_KO_rep3

address: 269 Campus Drvie

data_processing:
HiC-pro pipeline is used to align and generate contact matrix
FitHiChIP is used to call loops and differential loops
HiC file is generate using juicer_tools pre command
Assembly: hg38
Supplementary files format and content: hic file
Library strategy: HiChIP

extract_protocol:
Cells were removed from the plate and singularized with Accutase.
Cohesin HiChIP library prep was performed as previously described (Mumbach et al., 2016). Briefly, 25x106 cells were crosslinked and digested with MboI (NEB). After digest, biotin was incorporated into the sticky ends of fragments before ligation. Cohesin ChIP was performed to enrich for proximity ligations bound to cohesin, using an SMC1 antibody (Bethyl, A300-055A). The paired-end library quality was assessed on a MiSeq sequencer before sequencing on an Illumina HiSeq 4000. Three replicates were pooled and sequenced across two HiSeq lanes for a total of 1200 million reads per sample.

value: AP2a KO

value: Cohesin


title: high target, g11, rep 3 [XP006]

source_name: HEK293T_high target_g11

value: high target_g11


title: SNB-75_SSIII-DM-treated_2

tag: cell type