title: PRO-seq SW480 Rep2

city: Chicago

first: Mannan

last: Bhola

address: 303 E Superior St

department: BMG

institute: Northwestern university

description:
Nascent RNA
PRO_M.bw

data_processing:
The low-quality reads were removed using Trim_Galore (v0.6.10 with cutadapt v4.2) with the following parameters: --clip_R1 10 --clip_R2 3 --three_prime_clip_R1 2 --three_prime_clip_R2 2. Sequencing reads were mapped to the hg38 human genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fa) using bwa-mem (v0.7.17) with default parameters. SAMtools v1.14 was used for filtering the mapping quality and the duplicate reads. Only high-quality reads (both ends uniquely mapped, passed quality check, no PCR duplicates, properly paired, and with mapping quality score  30) were used for further analysis. deepTools (v3.5.1) was used to generate normalized BigWig files.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: SW480 Cells

growth_protocol: Human SW480 cells were grown at 37°C, supplied with 5% CO in Dulbeccos modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
Nuclei from SW480 cells were isolated and snap-frozen in storage buffer [10 mM tris-HCl (pH 8.0), 25% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 5 mM dithiothreitol (DTT)]. Next, 10 × 1M nuclei and 100 l of storage buffer were run on by the addition of 100 l of prewarmed 2× reaction buffer [10 mM tris-HCl (pH 8.0), 300 mM KCl, 5 mM MgCl2, 1% sarkosyl, 1 mM DTT, RNaseOUT (0.8 U/l; ThermoFisher Scientific), 250 M adenosine 5-triphosphate,250 Mguanosine 5-triphosphate,50 M biotin-11cytidine 5-triphosphate (PerkinElmer), and 50 M biotin-11uridine 5-triphosphate (PerkinElmer)]for 3 min at 37°C. Reactions were stopped by the addition of 500 l of TRIzol LS (Invitrogen) and purified following the manufacturers instructions. RNAs were heat-denatured at 65°C for 40s, placed on ice, and fragmented with 0.2 N of NaOH on ice for 10 min. After pH adjustment with 1M tris-HCl (pH 6.8), buffer exchange using P-30 columns (Bio-RadLaboratories) was performed.
The 3 RNA adaptor (VRA3:5-GAUCGUCGGACUGUAGAACUCUGAAC-/inverted dT/-3) was ligated to the eluted RNAs, and a second biotin RNA enrichmentwas performed as described above. Next, the 5 end of RNA swas enzymatically modified with RNA 5 pyrophosphohydrolase(NEB), and hydroxyl repair was performed using T4 polynucleotidekinase (NEB). Purified RNAs were subsequently ligated with the 5RNA adaptor (RA5: 5-CCUUGGCACCCGAGAAUUCCA-3).A third biotin RNA enrichment was performed before reverse transcription of the eluted RNAs. Libraries from two biological replicates were amplified for 13 cycles, size-selected for 140 to 350 bp, and paired-end sequenced on Illumina HiSeq 4000 (75 bp).

treatment_protocol: SW480 cells were transduced with viral supernatants containing 8 μg ml-1 polybrene (Sigma-Aldrich). After 8h infection, virus-containing medium was removed and replaced with fresh medium. After 48 h, the cells were selected using puromycin at a final concentration of 1.5 μg ml-1 before harvesting the cells for sequencing

value: SW480 Cells


title: Ribo_HS_0.5

status: Public on Jul 10 2024

type: SRA

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero, Ribo-FilterOut_Ribo-Calibration

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms
Library strategy: Ribo-seq

molecule: total RNA

organism: Homo sapiens

source_name: cultures

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer.
Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer.
The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice.
S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer.
E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker.
For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.
0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

tag: cell line

tag: tissue

value: cultures

tag: cell type

value: Human Embryonic Kidney cells293

tag: rrna depletion

value: Ribo zero and Ribo-Filterout

tag: treatment

value: Heatshock 0.5 h


title: Ribo_HEK_Ribo_zero_2

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero

value: WT

value: Ribo zero


title: PPGS-Vector-1 (RNA-seq)

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3
Data were pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab delimited text file containing raw counts
Supplementary files format and content: tab delimited text file containing rlog normalized counts

organism: Mus musculus

source_name: breast tumor

growth_protocol: CCN6KOT primary Cells were growth in DMEM/F12  10%FBS and transduced with lentivirus  of DNTCF4 construct and control followed by  puromycin selection

extract_protocol:
Cells were collected   trypsin and then RNA extracted using QIAGEN RNA protocol.
Qiagen RNA protocol for cells.

treatment_protocol: treatment with puromycin

value: breast tumor

value: Breast Cancer cell line

tag: condition

value: Spindle Metaplastic

value: lentivirus Control


title: PRO-seq SW480 Rep1

state: IL

description:
Nascent RNA
PRO_M.bw


title: Q08B047467NA3

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Illumina DRAGEN BCL, then fastq files were analysed with salmon to get counts data. The counts were imported to DESeq2.
Assembly: GRCh38
Supplementary files format and content: DESeq2 normalised counts

source_name: bone

growth_protocol: These are FFPE samples of the osteosarcoma.

extract_protocol:
The formalin-fixed paraffin-embedded tissue (FFPE) samples (n=90: 50 OS + 40 normal) were obtained through PathWest Nedlands (QEII Medical Centre, Australia) and total RNA was extracted using the Norgen FFPE RNA purification kit (#25300) using manufacturer’s standard protocol. The purified RNA samples were sent to the Australian Genome Research Facility (AGRF) in Melbourne for sequencing.
whole transcriptome library preparartion with ribominus depletion for rRNA

value: bone

tag: disease state

value: NORMAL

tag: Sex

value: M

value: chemosurg

tag: status

value: alive

tag: ageatdiagnosis


title: OCM1-shControl_rep3

city: Shanghai

first: Man

last: Xiao

address: No.24, Lane 1400, Beijing West Road

department: Department of Clinical Laboratory

country: China

institute: Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University

description: Sample 6

data_processing:
Illumina Casava software1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie 2 v2.1.0.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample1, Sample2, Sample3, Sample4, Sample5, and Sample6.

extract_protocol:
A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARL4C Wild Type


title: Q08B047467NA18

value: TUMOUR


title: PRI_GVC1 (EP) [EP_3367]

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCh38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: hg38
Supplementary files format and content: Counts

source_name: Brain

growth_protocol: GVC were maintained in Endothelial Growth media supplemented with 2% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37*C. GBM cells were maintained in DMEM:F12 with B27 minus vitamin A, and supplemented with FGF, EGF and heparin plus antibiotics

extract_protocol:
Total RNA was extracted using Qiagen RNEasy microkit.
Library was prepared using TruSeq Stranded RNA (100ng) +Ribozero Gold.
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end, 2X75bp with Illumina Hiseq 4000

treatment_protocol: No treatment was performed on these cultures

value: Brain

value: TEC

value: endothelial


title: Ribo_HS_CT2

value: cultures

value: Human Embryonic Kidney cells293

value: Ribo zero and Ribo-Filterout

value: control condtion


title: Ribo_HS_CT1


title: Q05B030211MA29

value: chemo


title: MLN, D30, i.n. boost

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

library_source: transcriptomic single cell

data_processing:
The raw fastq files were mapped to the 10x Genomics pre-built mm10 genome reference (2020-A), and the raw count matrices were generated with Cell Ranger v6.0.2
Assembly: mm10
Supplementary files format and content: hdf5 files include raw count for each sample

source_name: MLN

extract_protocol:
Lungs, spleen, and MLN were harvested from mice that received DNA-OVA i.m. prime plus LAIV-OVA i.n. boost vaccination at designated time points. Red blood cells were removed, and total single cells were collected and proceeded to the dead cell removal (following the instruction of Dead Cell Removal Kit, Miltenyi Biotec). 2×104 live cells were subsequently proceeded to the downstream scRNA-seq library construction.
Library was performed according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index), 10X genomics.

value: MLN

value: DNA-OVA i.m./EP plus LAIV-HK68-OVA i.n.


title: OCM1-shControl_rep2

description: Sample 5


title: Lung, D30, i.n. boost

source_name: Lung

value: Lung


title: Q05B009812WA32

value: bone

value: NORMAL


title: OCM1-shControl_rep1

description: Sample 4


title: Q05B009812WA29

value: M

value: chemosurg


title: Spleen, D4, i.n. boost

source_name: Spleen

value: Spleen


title: RNA_RocA0.3μM2

description: RNAseq_and_rRNA_depletion_with_Ribo-Zero_Ribo-Calibration

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms

value: 0.3 uM RocA


title: MLN, D4, i.n. boost


title: OCM1-shARL4C_rep3

description: Sample 3

value: ARL4C Knockdown with shRNA


title: Q05B005169WA1

value: F

value: alive


title: RNA_RocA0.3μM1

value: cultures


title: OCM1-shARL4C_rep1

description: Sample 1


title: Q05B005169WB7

value: TUMOUR


title: Q04B025963TB28


title: Spleen, D2, i.n. boost


title: Lung, D4, i.n. boost


title: Q04B025963TA1


title: Spleen, D30, i.n. boost


title: OCM1-shARL4C_rep2

description: Sample 2


title: MLN, D2, i.n. boost


title: nickel, root, rep1

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

country: France

institute: CNRS

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate the transcriptome assembly (Lhav_transcriptome_v2), paired-end reads originating from in vitro sample of L. havanensis  roots and shoots grown in presence of nickel (Lhav_Ni_F, Lhav_Ni_R) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 25. Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Lhav_transcriptome_v2 using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Assembly: Lhav_transcriptome_v2.fasta
Supplementary files format and content: Lhav_transcriptome_v2.fasta : annotated assembly of Leucocroton transcriptome, fasta format
Supplementary files format and content: Readcounts: readcounts table for each sample after mapping each sample to the Lhav_transcriptome_v2 reference, CSV format

molecule: polyA RNA

organism: Leucocroton havanensis

source_name: root

growth_protocol: L. havanensis was grown in vitro on Murashige & Skoog medium with agar containing 500 mg/L NiSO4 as described in González, D. A., & Matrella, S. (2013). Nickel hyperaccumulation “in vitro” by Leucocroton havanensis (Euphorbiaceae) / Hiperacumulación “in vitro” de Ni en Leucocroton havanensis (Euphorbiaceae). Revista Del Jardín Botánico Nacional, 34/35, 83–88. http://www.jstor.org/stable/43152813

extract_protocol:
Total RNA were extracted using TRIzol LS Reagent Method (Protocol#10, Johnson et al. 2012, PLoS ONE 7(11): e50226. doi:10.1371), and treated with DNAseI.
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Samples were first stabilized in RNAlater (Invitrogen) and then stored at -80°C before RNA extraction

value: root

value: nickel


title: Lung, D2, i.n. boost


title: nickel, shoot, rep1

description: re-analysis of GSM3208127

source_name: shoot

value: shoot


title: no nickel, shoot, rep1

value: no nickel


title: Ribo_RocA3μM2

value: Human Embryonic Kidney cells293

value: Ribo zero and Ribo-Filterout

value: 3 uM RocA


title: Spleen, D30, single i.n.

value: LAIV-HK68-OVA i.n.


title: MLN, D30, single i.n.

value: MLN


title: Q02B032169YB12

value: bone

value: NORMAL

value: chemo

value: deceased


title: no nickel, root, rep1


title: Q02B032169YB18

value: F


title: C_auris_200μM_HSL-3.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441 and C. albicans SC5314.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: genome: https://fungi.ensembl.org/_candida_auris_gca_002759435/Info/Index; features: http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes p , corrected p. fold change, log fold change values and raw data for each Samples

organism: Candidozyma auris

source_name: fungal cells

growth_protocol: The C. albicans SC5314 reference strain and C. auris isolate 12 (NCPF 8973), derived from the South Asian/Indian lineage, were used in this study. Both strains were maintained on YPD agar plates [YPD broth (VWR, 1% yeast extract, 2% peptone, 2% glucose) and 2% agar (VWR), pH 5.8)] at 37 °C.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Strains were pre-cultured in YPD broth overnight at 37 °C, diluted to an OD640 of 0.1 in YPD broth (20 mL aliquots in 100 mL Erlenmeyer flasks). Cultures were incubated at 37 °C and 140 rpm for 6 h. HSL (100 or 200 μM final concentration) was added after 4 h of incubation to the exponentially growing phase cultures. Samples were collected after 2 h HSL exposure then were washed three times with physiological saline. Total RNA was isolated from lyophilized fungal cells in three biological replicates.

value: fungal cells

tag: genotype

value: Isolate 12

value: 200 μM HSL treated


title: Q01B033022AB2

value: TUMOUR


title: Ribo_RocA3μM1

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut_Ribo-Calibration

value: cultures


title: Lung, D30, single i.n.

value: Lung


title: Spleen, D4, single i.n.

value: Spleen


title: MLN, D4, single i.n.


title: Ribo_RocA0.3μM2

value: Human Embryonic Kidney cells293

value: 0.3 uM RocA


title: T47D, FRMD3 KO,rep2

city: Beijing

first: Qianchen

last: Li

address: Beijing

institute: PKU

data_processing:
Hista2 for mapping sequence
Samtools for ordering sam file to bam file
FeatureCounts for counting gene reads
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Mammary gland

growth_protocol: MCF-7 (T47D)  cells were maintained in DMEM (1640) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysised with trizol to extract RNA.
3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 following manufacturer's protocols.

value: Mammary gland

value: FRMD3 KO


title: Ribo_RocA0.3μM1

value: Ribo zero and Ribo-Filterout


title: C_auris_200μM_HSL-2.


title: T47D, FRMD3 KO,rep1


title: Ribo_DMSO1

value: DMSO


title: Ribo_DMSO2


title: T47D, FRMD3 KO,rep3


title: Lung, D4, single i.n.

value: LAIV-HK68-OVA i.n.


title: C_auris_Control-6

value: untreated


title: Ribo_fly_ribopools_2

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools
Ribo_fly.csv

organism: Drosophila melanogaster

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer. Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer. The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice. S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer. E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker. For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.  0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)


title: C_auris_Control-5


title: T47D, WT,rep3

value: WT


title: Ribo_fly_ribopools_1


title: T47D, WT,rep2


title: C_auris_Control-4


title: T47D, WT,rep1


title: C_auris_200μM_HSL-1.


title: C_auris_100μM_HSL-3.

value: 100 μM HSL treated


title: Ribo_fly_CT_2

description:
Ribosome profiling_and_rRNA_depletion_with_None
Ribo_fly.csv


title: Lung, D2, single i.n.


title: Ribo_fly_CT_1


title: Spleen, D0

value: DNA-OVA i.m./EP


title: MCF-7, FRMD3 KO,rep2


title: Ribo_fly_ribopools_Ribo-Filterout_2

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools,Ribo-FilterOut
Ribo_fly.csv


title: C_auris_100μM_HSL-2.

value: fungal cells

value: Isolate 12


title: MLN, D0

value: MLN


title: C_auris_100μM_HSL-1.


title: Lung, D0


title: MCF-7, WT,rep3


title: Ribo_fly_ribopools_Ribo-Filterout_1


title: MCF-7, FRMD3 KO,rep1


title: Spleen, Naïve


title: Ribo_fly_Ribo-Filterout_1

description:
Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut
Ribo_fly.csv


title: MCF-7, WT,rep2


title: C_auris_Control-1


title: MLN, D2, single i.n.


title: Spleen, D2, single i.n.


title: MLN, Naïve


title: amplicon NOMe-seq in wt mES cells, rep2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
MiSeq 500bp paired-end
NOMe_PCRamplicon_wt_r2
PCR_Nome_matrix_MotifCentered.rds
amplicon NOMe-seq in wt mES cells, replicate 2

library_source: genomic

data_processing:
*library strategy: Nucleosome Occupancy and Methylome sequencing (NOMe-seq)
Barcoded samples were pooled and sequenced on an Illumina MiSeq instrument.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
umi_tools (version 1.0.1) were used to remove reads that contain identical UMIs, then reads were aligned using bisulfite aware mapping by Biscuit (v 0.3.16, opions: with the options -b 1 -f 0 -K NAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -J NAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).Methylation call extraction was performed using nomeR get_data_matrix_from_bins. This matrix was converted to a single cell experiment object upon import into dinoR for further analysis.
Assembly: mm10
Supplementary files format and content: Processed data files are methylation call matrices from nomeR saved as .rds files (R Data Serialization). One contains all replicates individually while the other contains averaged values of the replicates  ("replicatesMerged"). These files can be imported to dinoR for visulaization and analysis.

molecule: genomic DNA

source_name: embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
0.8*10e6 cells were harvested at the indicated time-points, washed and nuclei were treated with M.CviPI for methylation foot-printing. Then cells were lysed and DNA was isolated. 120ng DNA was dephosphorylated with rSAP and digested by Cas9 loaded with an in vitro transcribed guideRNA pool for the regions of interest.The digested DNA was used togenerate an NGS library. For a detailed protocol, please see Schwaiger et al, 2024.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit and xGen Methyl UDI-UMI (IDT) premethylated adapters. The library was bisulfite treated with the EZ DNA Methylation-Direct Kit, amplified using the KAPA HiFi Uracil+ (Roche) Kit, size selected with Ampure beads (targeting 300-600bp)and sequenced on an Illumina MISeq instrument in 600bp paired-end mode. For a detailed protocol, please see Schwaiger et al, 2024.

treatment_protocol: dTAG-13 was added to the culture medium at a final concentration of 0.5 uM. For wash-out, cells were washed twice in medium without dTAG-13 and then plated in fresh medium for recovery.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/46

value: wt


title: Lung, Naïve

value: Lung


title: MCF-7, FRMD3 KO,rep3


title: amplicon NOMe-seq in wt mES cells, rep1

description:
MiSeq 500bp paired-end
NOMe_PCRamplicon_wt_r1
PCR_Nome_matrix_MotifCentered.rds
amplicon NOMe-seq in wt mES cells, replicate 1

value: hybrid 129-C57BL/45


title: Cortex, Vehicle_4

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website 2 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: reference genome was built using Hisat2 v2.0.5 a
Supplementary files format and content: Tab-delimited txt file with FPKM

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
RNA was extracted using the Trizol reagent according to the manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification). The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Kidney

value: Cortex

value: Wildtype


title: C_auris_Control-3


title: Total RNA-seq DMSO treat rep2

description:
Total RNA-seq Ribo-Depletion
DMSO_Merge.raw.fwd.bw
DMSO_Merge.raw.rev.bw

data_processing:
The reads were trimmed for adapter contaminations and quality using Trim_Galore (v0.6.10 with cutadapt v4.2) with the following parameters: --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5. Paired-end raw reads were mapped to the hg38 human genome with GENECODE v43 (primary_assembly) using STAR aligner v2.7.9a with the following parameters: --genomeLoad NoSharedMemory --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --sjdbScore 1 --limitBAMsortRAM 60000000000 --outWigType wiggle --outWigNorm None. Only high-quality reads (both ends were uniquely mapped, pass quality check, and with mapping quality score >= 255) were kept for the analysis. The gene expression was determined with featureCounts (subread v1.6.1) using GENECODE v43 (primary_assembly) gene annotation with the parameters: -s 2 -B -p -t exon -g gene_id The gene counts were used to determine the differential gene expression with DESeq2 v1.36 and q-value<0.05 and a log2 fold change of 0.58.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cell Line

extract_protocol:
Total RNA was extracted from samples using TRIzol reagent (Invitrogen) according to the manufacturers instructions. For Chipseq, DNA samples were purified using UPrep® Spin Columns (Genesee Scientific).
Total RNA-seq (ribo-depleted) libraries for all samples were generated and sequenced by Admera Health. Briefly, isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Libraries were constructed with KAPA RNA HyperPrep with RiboErase (Roche, Indiana, USA) and performed based on manufacturers recommendations. Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). The final library size was about 430 bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 50 M PE reads per sample (25M in each direction).

value: SW480 Cells

value: DMSO


title: Total RNA-seq DMSO treat rep1


title: Total RNA-seq CPT treat rep2

description:
Total RNA-seq Ribo-Depletion
CPT_Merge.raw.fwd.bw
CPT_Merge.raw.rev.bw


title: Ribo_fly_Ribo-Filterout_2


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 24h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_24h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 24 hours recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/44


title: ABX AntiPDL1 & OGVehicle, rep 14

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

institute: Parean Biotechnologies

data_processing:
FastQC (version 0.11.9) and MultiQC (version 1.12) were used for quality control of raw paired-end fastq files.
Sequencing adaptors as well as low quality reads were trimmed out using Trimmomatic (version 0.39; Parameters used: NexteraPE-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36)
Transcript quantification was performed using Salmon (version 1.9.0) on trimmed fastqs against GENCODE M31 transcript reference database (assembly GRCm39)
Quantified transcripts were imported in R (version 4.2.2) using the package tximport (version 1.24.0)
Count data handling and differential analysis were performed using the package DESeq2 (version 1.36.0)
Genes were pre-filtered out if they expressed (count > 0) in less than 50% of samples
Assembly: GENCODE M31/GRCm39
Supplementary files format and content: tab delimited transcript quantification (Salmon output)

source_name: Tumor biopsies

extract_protocol:
RNA was extracted using Qiagen RNeasay kit following manufacturer instruction
mRNA library preparation were realized following manufacturer’s recommendations (Stranded Total RNA Prep Ligation with Ribo-Zero Plus from ILLUMINA). Final samples pooled library prep were sequenced on Novaseq 6000 ILLUMINA with S1-200 cycles cartridge (2x1600Millions of 100 bases reads) corresponding to 2x33Millions of reads per sample after demultiplexing.

value: Tumor biopsies

tag: strain

value: ABX AntiPDL1 & OGVehicle


title: Cortex, Oxo_5

value: High_salt_Oxonic acid


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 12h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_12h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 12 hours recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/42


title: ABX AntiPDL1 & OGVehicle, rep 13


title: Cortex, Vehicle_2


title: ABX AntiPDL1 & OGVehicle, rep 12


title: Total RNA-seq CPT treat rep1


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 24h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_24h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 24 hours recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/43


title: Cortex, Vehicle_3


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 12h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_12h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 12 hours recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/41


title: MCF-7, WT,rep1

value: Mammary gland

value: WT


title: Cortex, Vehicle_1


title: ABX AntiPDL1 & OGVehicle, rep 10


title: Total RNA-seq FHC Rep 4

description:
Total RNA-seq Ribo-Depletion
FHCM_merge2.raw.fwd.bw
FHCM_merge2.raw.rev.bw

value: FHC Cells


title: C_auris_Control-2

value: fungal cells

value: Isolate 12

value: untreated


title: Cortex, Vehicle_5

value: Kidney

value: Cortex


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 8h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_8h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 8 hours recovery in medium without dTAG13,  replicate 2

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/40


title: Total RNA-seq FHC Rep 3


title: Cortex, Oxo_4

value: Wildtype


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 8h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_8h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 8 hours recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/39


title: ChIP-seq RNA PolII SW480_shTOP1 Rep 1

description:
ChIP-seq
TOP1KD_POL2_over_input.bw
RNAPII_KD_over_SCR.bw

data_processing:
The low-quality reads were removed using Trim_Galore (v0.6.10 with cutadapt v4.2) with the following parameters: --clip_R1 3 --clip_R2 3 --three_prime_clip_R1 3 --three_prime_clip_R2 3 for paired-end reads and --clip_R1 3 --three_prime_clip_R1 3 for single-end reads. Sequencing reads were mapped to the hg38 human genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fa) using bwa  v0.7.17 (mem for paired-end reads, aln and samse for single-end reads) and default parameters. SAMtools v1.14 was used for filtering the mapping quality and the duplicate reads. Only high-quality reads (uniquely mapped, pass quality check, no PCR duplicates, and with mapping quality score >= 30. For paired end reads, we further required properly paired and both ends uniquely mapped) were used for further analysis. Spike-in normalization was performed by mapping the reads to the Drosophila melanogaster genome (dm6) using bwa mem with the same parameters. Deeptools v3.5.1 was used to generate normalized bigwig files by combining reads from two replicas. The bins per million mapped normalized reads were used and the log2 ratio between the ChIP-seq signal over Input was calculated.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cell resuspensions were next dounced ten times in a prechilled glass homogenizer. Nuclei were collected and resuspended in shearing buffer (0.1% SDS, 0.5% N-lauroylsarcosine, 1% Triton X-100, 10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1 mM PMSF, PICs) and incubated on ice for 30 min. Chromatin was fragmented using an E220 Focused-Ultrasonicator (Covaris) to an average size of 200-600 bp.
ChIP-seq libraries for all samples were generated and sequenced by Admera Health. Briefly, immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep (Roche, Basel, Switzerland) following the manufacturers recommendations. All samples were subjected to end-repair, adaptor ligation followed by indexed PCR using Illumina® 8-nt dual-indices. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay and Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA). Final libraries were quantified using QuantStudio ® 5 System (Applied Biosystems, California, USA) prior to equimolar pooling based on qPCR QC values. Sequencing was performed on an Illumina NovaSeq (Illumina, CA, USA) with aread length configuration of 150 PE for 40 M PE reads 20 M in eachdirection) per sample. For TOP1cc-seq and RNA PolII CHIP-seq, the read length configuration was 75 SE.

treatment_protocol: The cells were cross-linkedwith 2 mM disuccinimidylglutarate (ProteoChem) for 30 min, followed by cross-linkingwith1% formaldehyde for an additional 10 min at room temperature andquenched with 125 mM glycine (Thermo Fisher Scientific) for 5 min.Cell pellets were resuspended in lysis buffer [20 mM tris-HCl(pH 7.5),300 mM NaCl, 2 mM EDTA, 0.5% NP-40,1% Triton X-100,1 mMPMSF, and PICs] and incubated on ice for 30 min.

value: SW480 Cells with shRNA TOP1


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 4h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_4h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 4 hours recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/38


title: Cortex, Oxo_3

value: High_salt_Oxonic acid


title: ABX AntiPDL1 & OGVehicle, rep 9

value: Tumor biopsies

value: ABX AntiPDL1 & OGVehicle


title: ABX AntiPDL1 & OGVehicle, rep 8


title: ChIP-seq RNA PolII SW480_shTOP1 Rep 2


title: ABX AntiPDL1 & OGVehicle, rep 7


title: Cortex, Oxo_2


title: ABX AntiPDL1 & OGVehicle, rep 11


title: Cortex, Oxo_1


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 2h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_2h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 2 hours recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/35


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 2h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_2h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 2 hours recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/36


title: ChIP-seq Input SW480_shTOP1 Rep 1


title: ChIP-seq Input SW480_shTOP1 Rep 2


title: ABX AntiPDL1 & OGVehicle, rep 6


title: ChIP-seq RNA PolII SW480_shCTL Rep 2

description:
ChIP-seq
SCR_POL2_over_input.bw
RNAPII_KD_over_SCR.bw

value: SW480 Cells with shRNA Control

value: Control


title: ABX AntiPDL1 & OGVehicle, rep 4


title: ABX AntiPDL1 & OGVehicle, rep 5


title: Reln-S6

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v7.1.0 with the associated Ensembl gene transfer format (gtf) file (version 105). CellRanger filtered outputs were analyzed with Seurat v4.3.0.1 using R v4.3.1.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.4.3.0.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome (5,846 nuclei post-processing). The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed.
For each sample, we used Seurat to determine the 3,000 genes with highest cell-to-cell variability; these sets of genes were used to identify “anchor” pairs of cells between samples with a shared pattern of gene expression. We then integrated the eight individual datasets based on the identified anchors, using the first 17 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We used Seurat for initial dimensionality reduction and clustering as detailed below. We first performed dimensionality reduction via PCA retaining 17 PCs, followed by UMAP with the 17 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.3. After initial clustering but before differential gene expression analysis, we used DoubletFinder v.2.0.3 to identify and remove heterotypic doublets, a consequence of two cells of different types being captured in a single droplet and thus presenting as a single heterotypic “cell.” We assumed a doublet formation rate of 4% based on 8,000 cells loaded per GEM well, as indicated in the 10x Genomics library preparation documentation. After removing doublets, we repeated the dimensionality reduction and clustering steps detailed above. We matched the resulting clusters to specific cell types based on known marker genes from previous work
To identify genes differentially expressed between Reln knockdown and lacZ controls, we conducted a differential expression analysis on a pseudobulked gene expression matrix created by summing counts for each gene within a sample (or single GEM well) and across cells within each cell type. Genes with mean counts <5 were removed. Differential expression analysis was conducted with DESeq2 v.1.40.2 using a likelihood ratio test (LRT) with treatment condition as the main effect and controlling for the effect of sex to ensure that identified significant differential expression could be attributed to the treatment and not confounded by differences in response between sexes. To assess differential expression among cell types, we conducted a separate LRT with cell type as the main effect and controlling for sex.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

source_name: nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
Brains were blocked in 1mm sections, and NAc punches were obtained, flash frozen, and stored at -80°C prior to nuclei isolation. 1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 2mm punch tool centered on the nucleus accumbens core subregion, and frozen for storage. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from one rat was transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplification, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry) on the Chromium iX instrument. Libraries were constructed according to manufacturer's instructions using the Chromium Single Cell 3′ Library Construction Kit (10× Genomics, PN-1000190). Nuclei (6,221 total) from adult rat NAc were sequenced on the Illumina NovaSeq6000 at the UAB Heflin Genomics core to a depth of ~300,000 reads per nuclei.

treatment_protocol: Rats underwent stereotaxic surgery to transduce nucleus accumbens tissue with lentiviruses expressing CRISPRi machinery targeting lacZ (as a control) or Reln. Two weeks following surgery, animals (4 lacZ, 4 Reln 2M/2F per group) were euthanized prior to rapid decapitation.

value: Sprague-Dawley

tag: age

value: 90-120 days old

value: nucleus accumbens

value: Female

value: Reln sgRNA


title: Reln-S7

value: Male


title: Reln-S2


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 1h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_1h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 1 hour recovery in medium without dTAG13,  replicate 1

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/33


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 4h recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_4h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 4 hours recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/37


title: ABX AntiPDL1 & OGVehicle, rep 3


title: ChIP-seq RNA PolII SW480_shCTL Rep 1


title: ABX AntiPDL1 & OGVehicle, rep 2


title: Reln-S4


title: ABX AntiPDL1 & OGVehicle, rep 1


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 1h recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_1h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 1 hour recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/34


title: lacZ-S8

value: lacZ sgRNA


title: ChIP-seq Input SW480_shCTL Rep 2


title: ABX AntiPDL1 & EXL01, rep 13

value: Tumor biopsies

value: ABX AntiPDL1 & EXL01


title: lacZ-S1


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_12h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/30


title: X8i

data_processing:
Raw FASTQ files were processed using nf-core/rnaseq v3.10 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows using a pipeline executed with Nextflow v23.04.1.
Splice-aware alignment to the mRatBn7.2/Rn7 genome assembly was conducted using STAR v2.7.9a with the associated Ensembl gene transfer format (gtf) file (version 105).
Binary alignment map files were indexed with SAMtools (v1.16.1). Gene-level counts were generated using featureCounts (Rsubread v2.0.1)
QC metrics were collected and reviewed with MultiQC (v1.13), and a minimum of 20M mapped reads were obtained per sample (range: 22.6M to 121.4M)
Differential expression testing was conducted using DESeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini–Hochberg method, and DEGs were designated as those genes with an adjusted p-value <0.05. Genes with unreliable/low expression estimates (basemean <50) were excluded from subsequent analysis.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Count_matrix.txt contains RNA-seq count values for annotated gene for each sample

source_name: Sprague-Dawley

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 12 days prior transduction with CRISPRi lentivirus components. RNA was extracted at DIV 19 and RNA-seq was performed using mRNA.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBNext Poly(A) mRNA manetic isolation module was used to enrich polyadenylated RNA. RNA-seq libraries underwent sequencing (100 bp paired-end directional reads) on an Illumina sequencing platform (NovaSeq6000).

treatment_protocol: Primary rat striatal neurons were transduced with lentiviruses expressing CRISPRi machinery on DIV12 with a multiplicity of infection (MOI) per cell of 2000 for each virus.

value: Embryonic day 18, 19 DIV

tag: source

value: Striatum


title: ABX AntiPDL1 & EXL01, rep 12


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 4 hours dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_4h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 4 hours dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/28


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 30min recovery,  rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_30min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 30 minutes recovery in medium without dTAG13,  replicate 2

value: hybrid 129-C57BL/32


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_12h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/29


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12h dTAG13 treatment followed by wash-out and 30min recovery,  rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_washout_30min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 12 hours dTAG13 treatment, i.e. ADNP depletion, followed by a wash-out and 30 minutes recovery in medium without dTAG13,  replicate 1

value: hybrid 129-C57BL/31


title: lacZ-S5

value: Sprague-Dawley

value: 90-120 days old

value: nucleus accumbens

value: Female


title: MDA_MB_231 cells,Knockdown,RBM7,sh2

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Breast

growth_protocol: MDA-MB-231 cells were cultured without nitrogen dioxide at 37℃ in Leibovitz’s L-15 medium contained 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast

value: Breast cancer cells


title: ABX AntiPDL1 & EXL01, rep 11


title: MDA_MB_231 cells,Knockdown,Ctl


title: ChIP-seq Input SW480_shCTL Rep 1

value: SW480 Cells with shRNA Control

value: Control


title: MDA_MB_231 cells,Knockdown,RBM7,sh1


title: lacZ-S3

value: lacZ sgRNA


title: MDA_MB_231 cells,Overexpression,MFGE8-L


title: ABX AntiPDL1 & EXL01, rep 10

value: Tumor biopsies

value: ABX AntiPDL1 & EXL01


title: ABX AntiPDL1 & EXL01, rep 9


title: MDA_MB_231 cells,Overexpression,MFGE8-S


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 2 hours dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_2h_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 2 hours dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/26


title: X7i

value: Embryonic day 18, 19 DIV

value: Striatum

value: Reln sgRNA


title: MDA_MB_231 cells,Overexpression,Ctl


title: X6i


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 2 hours dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_2h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 2 hours dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/25


title: ABX AntiPDL1 & EXL01, rep 8


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 4 hours dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_4h_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 4 hours dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/27


title: X5i

value: Sprague-Dawley


title: Ribo_HEK_CT2_1000

description:
Ribosome profiling_and_rRNA_depletion_with_ribo_pools
Ribo_human.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms
Library strategy: Ribo-seq

value: 1000mM NaCl wash


title: ABX AntiPDL1 & EXL01, rep 7


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 60 minutes dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_60min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 60 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/24


title: ABX AntiPDL1 & EXL01, rep 6


title: X2i


title: X4i


title: Ribo_HEK_CT1_300

value: 300mM NaCl wash


title: ABX AntiPDL1 & EXL01, rep 5


title: ABX AntiPDL1 & EXL01, rep 3


title: Ribo_HEK_CT2_300


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 60 minutes dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_60min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 60 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/23


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 45 minutes dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_45min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 45 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/22


title: Ribo_HEK_CT1_1000


title: ABX AntiPDL1 & EXL01, rep 2


title: X1i


title: Ribo_HEK_CT2_100

value: 100mM NaCl wash


title: X3i

value: lacZ sgRNA


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 45 minutes dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_45min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 45 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/21


title: Ribo_HEK_CT1_100


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 30 minutes dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_30min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 30 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/20


title: Sham_3

first: Debao

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

description: undergo sham operation at postnatal day 1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: GCA_000001895.4
Supplementary files format and content: FPKM

source_name: Pulmonary vein

growth_protocol: The suckling rats were breastfed by the mother rats and were housed in groups of 8-10 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
Pulmonary vein tissue from the upper lobe of the right  lung was rapidly removed from executed rat and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Newborn rats were anesthetized by brief hypothermia on crushed ice for approximately 3 minutes and then transferred to an ice bed to maintain anesthesia during the surgery. The operation was performed under the stereomicroscope in the supine position, including sternum clipping, thoracic cavity opening, pulmonary vein quantitative constriction, thoracic cavity closing, etc. The constriction procedure which was only performed in the pulmonary vein group. After the surgery was completed, the rats were removed from the ice bed and placed on a heat plate of 37℃ to warm and wake up. The pups were not put back to their moms until they were absolutely conscious (around 3h after surgery).

value: Pulmonary vein

value: SD

tag: developmental stage

value: Postnatal day 21

value: Wild type

value: sham operated


title: Sham_2


title: DS06_CL_1

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

institute: University of Western Australia

description:
cell line
NovaSeq 6000 SP 200 cycles reagent kit (Illumina)

data_processing:
Sample demultiplexing and QC (MultiQC) were performed by Genomics WA.
FastQ files were trimmed using Trim Galore package before alignment (GENECODE v34, GRCh38.p13 assembly, as reference)
Quantification (transcript per million – TPM) were performed using Kallisto.
Gene filtering, raw count transformation (regularised log -rlog) and differential expression analysis were performed with the DESeq2 package (v 1.41.4)
Assembly: GENECODE v34, GRCh38.p13 assembly
Supplementary files format and content: counts_tpm.txt

growth_protocol: Human DS-ALL cells harvested from PDX models were cultured in ‘complete’ RPMI1640 media supplemented with 2 mM L-glutamine, 50 µM 2-mercaptoethanol, penicillin (100 U/ml)-streptomycin (100 µg/ml), 1X non-essential amino acids, 1 mM sodium pyruvate (all from Invitrogen) and 20% heat inactivated foetal calf serum (FCS) (Cell Sera, Australia). The DS-PER961 cell line was cultured with recombinant human IL-7 (10 ng/mL), and the DS-PER962 cell line with human FLT3 ligand (10 ng/mL) (Peprotech and STEMCELL Technology). Cell lines were cultured at 37oC, in 5% CO2 with 95% humidity (Heracell VIOS 160i incubator).

extract_protocol:
Total RNA was isolated from cells derived from freshly harvested cells from DS-ALL cell lines and PDXs using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA integrity, quality and quantity were measured by TapeStation RNA ScreenTape (Agilent), Nadodrop and Qubit RNA BR Assay Kit (ThermoFisher), respectively.  All samples had a RIN number > 9.5.
500 ng of total RNA (RIN >9.5) per sample were used as input for library preparation using the SureSelect Stranded PolyA RNASeq kit (Agilent), according to manufacturer's instructions by Genomics WA.

value: Down Syndrome ALL

value: KRAS G12S mutant

value: no treatment


title: ABX AntiPDL1 & EXL01, rep 1

value: Tumor biopsies

value: ABX AntiPDL1 & EXL01


title: ABXfree AntiPDL1 & OGVehicle, rep 8

value: ABXfree AntiPDL1 & OGVehicle


title: DS06_PDX_1

description:
PDX
NovaSeq 6000 SP 200 cycles reagent kit (Illumina)


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 15 minutes dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_15min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 15 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/17


title: Sham_1


title: PVS_3

description: undergo pulmonary vein banding operation at postnatal day 1

value: pulmonary vein banding


title: ABXfree AntiPDL1 & OGVehicle, rep 7


title: DS02_CL_21

value: CRLF2 + and JAK2 I682F mutant


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 5 minutes dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_5min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 5 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/16


title: ABXfree AntiPDL1 & OGVehicle, rep 5


title: PVS_2


title: DS02_PDX_18


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 5 minutes dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_5min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 5 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/15


title: Blood ZCCHC8 cases RNAseq3

city: London

first: Hemanth

last: Tummala

state: London

address: Blizard Institute

department: Genomics and Child Health

country: United Kingdom

institute: QMUL

data_processing:
The reads were processed and mapped following Lexogen Bluebee pipeline. The bam files were sorted and indexed uisng samtools. The sorted bam files were merged for sample groups (Controls and ZCCHC8 cases), sorted and indexed and converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --binSize 20 –normalizeUsing RPKM --smoothLength 60 --extendReads 150 --centerReads options. For differential gene expression analysis, counts were obtained through featurecounts tool in subread package followed by DESeq analysis.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: text files for RNAseq counts matrix and DESeq results

source_name: Whole Blood

extract_protocol:
RNA was isolated using an RNeasy mini kit (Qiagen Cat no: 74106).
RNA seq library was prepared using NEBNext Ultra II directional RNA library preparation kit (NEB cat no: E7760L) by following the manufacturer's protocol. Libraries were sequenced as 150 bp paired-end reads using Novaseq 6000.

treatment_protocol: Whole blood was taken from consented patients in PAXgene tubes

value: Whole Blood


title: PVS_1

value: Pulmonary vein

value: SD


title: Blood ZCCHC8 cases RNAseq2


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 30 minutes dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_30min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 30 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/19


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells before dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_0min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells before dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/14


title: ABXfree AntiPDL1 & OGVehicle, rep 1


title: ABXfree AntiPDL1 & OGVehicle, rep 2


title: Ribo_plant_ribopools_2

first: Shintaro

address: 2-1, Hirosawa

institute: RIKEN

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools
Ribo_plant.csv

organism: Arabidopsis thaliana


title: Ribo_plant_ribopools_1


title: ABXfree OGVehicle, rep 10

value: ABXfree OGVehicle


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells before dTAG13 treatment, i.e. ADNP depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_0min_r1
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells before dTAG13 treatment, i.e. ADNP depletion, replicate 1

value: hybrid 129-C57BL/13


title: guidedNOMe-seq in Ctcf-FKBP12(F36V) mES cells after 24h dTAG13 treatment, i.e. CTCF depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Ctcf_dTAG_r2
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in Ctcf-FKBP12(F36V) mES cells after 24h dTAG13 treatment, i.e. CTCF depletion, replicate 2

value: hybrid 129-C57BL/11


title: guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 15 minutes dTAG13 treatment, i.e. ADNP depletion, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_Adnp_dTAG_15min_r2
Nome_matrix_Adnp_timecourse.rds
Nome_matrix_Adnp_timecourse_replicates_merged.rds
guidedNOMe-seq in Adnp-FKBP12(F36V) mES cells after 15 minutes dTAG13 treatment, i.e. ADNP depletion, replicate 2

value: hybrid 129-C57BL/18


title: Blood Control RNAseq3

value: control


title: Ribo_plant_CT_2

description:
Ribosome profiling_and_rRNA_depletion_with_None
Ribo_plant.csv


title: ABXfree OGVehicle, rep 9

value: Tumor biopsies


title: Ribo_plant_CT_1


title: ABXfree OGVehicle, rep 8


title: Blood Control RNAseq2


title: Ribo_plant_ribopools_Ribo-Filterout_2

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools,Ribo-FilterOut
Ribo_plant.csv


title: Blood Control RNAseq1


title: ABXfree AntiPDL1 & OGVehicle, rep 3

value: ABXfree AntiPDL1 & OGVehicle


title: Blood ZCCHC8 cases RNAseq1


title: guidedNOMe-seq in Adnp knock-out mES cells, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_AdnpKO_r2
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in Adnp knock-out mES cells, replicate 2

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/9


title: Ribo_plant_ribopools_Ribo-Filterout_1


title: ABXfree OGVehicle, rep 7


title: IPF Explant 1

city: San Francisco

first: Max

last: Cohen

address: 513 Parnassus Ave, Box 0111

department: Medicine

institute: UCSF

description: IPF Explant 1

data_processing:
Raw output files were demultiplex and aligned to human transcriptome using 10x Cell Ranger pipeline
Assembly: GRCh38
Supplementary files format and content: 10x filtered feature/barcode/count matrices

extract_protocol:
Freshly obtained human lung was digested with dispase and collagenase, filtered, and flow-sorted for live epithelium and or mesenychme
Library construction was performed according to 10x Chromium 3' protocol

treatment_protocol: Patients with fibrotic lung disease were enrolled to take EGCG 600mg by mouth once daily for two weeks prior to surgical lung biopsy

value: Lung

value: Epithelium, mesenchyme

value: end-stage IPF explant

tag: sample type

value: End-stage explant from idiopathic pulmonary fibrosis


title: guidedNOMe-seq in wt mES cells, rep2

description:
MiSeq v3 600bp paired-end
gNOMe_wt_r2
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in wt mES cells, replicate 2

tag: cell line

value: hybrid 129-C57BL/7

value: wt


title: Normal Donor 1

description: Normal Donor 1

tag: tissue

value: healthy

value: Normal Lung


title: guidedNOMe-seq in wt mES cells, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_wt_r1
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in wt mES cells, replicate 1

value: hybrid 129-C57BL/6


title: guidedNOMe-seq in Adnp knock-out mES cells, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_AdnpKO_r1
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in Adnp knock-out mES cells, replicate 1

value: hybrid 129-C57BL/8


title: Ribo_plant_Ribo-Filterout_1

last: Iwasaki

description:
Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut
Ribo_plant.csv


title: Ribo_plant_Ribo-Filterout_2


title: ABXfree OGVehicle, rep 5

value: ABXfree OGVehicle


title: ABXfree OGVehicle, rep 4


title: Amel_adult_antenna_dsx_stop_stop_worker_biol rep3

city: Düsseldorf

first: Anna

last: Wagner

address: Universitätsstraße 1

department: Evolutionary Genetics

country: Germany

institute: Heinrich-Heine University

data_processing:
Use of the bcl2fastq2 conversion software (v2.20.0.422): Convert bcl files to fastq files, adapter trimming and demultiplexing. Mapping of the reads was performed using the kallisto software tool (Bray et al., 2016) to the Apis mellifera transcriptome (NCBI assembly Amel_HAv3.1). Use of the transcripts per kilobase million (TPM) method (Wagner et al., 2012) to normalise read counts. Calculation of gene expression differences using DESeq2 (Love et al., 2014).
Assembly: Amel_HAv3.1
Supplementary files format and content: tab-delimeted text file includes the adjusted P-values

organism: Apis mellifera

source_name: antennae

extract_protocol:
RNA was isolated from the antennae of workers with the dsx stop/stop mutation and wild-type workers using TRIZOL reagent as described in Vleurinck et al., 2016. RNA extracts from 5 bees were pooled for each of 3 biological replicates and genotype.
Library were prepared using 500 ng RNA and the "VAHTS Universal RNA-Seq Library Prep Kit for Illumina V6 with mRNA capture module version 7.0" (Vazyme Biotech co.). After normalisation of the bead-purified libraries, sequencing was performed on the HiSeq 3000/4000 system (Illumina Inc.) with a read setting of SR 1x150 bp.

value: antennae

value: dsx stop/stop


title: guidedNOMe-seq in Ctcf-FKBP12(F36V) mES cells after 24h dTAG13 treatment, i.e. CTCF depletion, rep1

description:
MiSeq v3 600bp paired-end
gNOMe_Ctcf_dTAG_r1
Nome_matrix_WT_AdnpKO_CtcfKD.rds
Nome_matrix_WT_AdnpKO_CtcfKD_replicatesMerged.rds
guidedNOMe-seq in Ctcf-FKBP12(F36V) mES cells after 24h dTAG13 treatment, i.e. CTCF depletion, replicate 1

value: hybrid 129-C57BL/10


title: Control Biopsy 4

description: Control Biopsy 4

tag: cell type

value: fibrotic lung disease

value: Biopsy


title: Plasma from unaffected, 555p

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
miND pipeline by TAmiRNA (Diendorfer et al.)
Assembly: GRCh38
Supplementary files format and content: raw miRNA reads CSV quantified with miND pipeline

source_name: sodium heparin plasma

extract_protocol:
Total RNA and miRNA from tissue and cells was isolated using the RNeasy Mini Kit (Qiagen)
Library miR preparation was performed using CleanTag™ Small RNA Library Preparation Kit

value: sodium heparin plasma

value: unaffected


title: Plasma from unaffected, 648p


title: Amel_adult_antenna_dsx_stop_stop_worker_biol rep2


title: Control Biopsy 3

description: Control Biopsy 3

source_name: Lung

value: Lung

value: Epithelium


title: ABXfree OGVehicle, rep 3

value: Tumor biopsies


title: Plasma from unaffected, 612p


title: ABXfree OGVehicle, rep 2


title: Amel_adult_antenna_dsx_stop_stop_worker_biol rep1


title: Plasma from HGPS, 204

value: HGPS


title: EGCG Biopsy 3

description: EGCG Biopsy 3

value: Epithelium, mesenchyme

value: EGCG


title: ABXfree OGVehicle, rep 6


title: ABXfree OGVehicle, rep 1


title: EGCG Biopsy 2

description: EGCG Biopsy 2


title: Amel_adult_antenna_control_worker_biol rep3

value: WT


title: EGCG Biopsy 1

description: EGCG Biopsy 1


title: Neutrophils in the bronchoalveolar lavage fluid (BALF) of  WT mice,virus, biological replicate 2

city: 北京

first: Yue

last: Wang

address: 新街口外大街19号

institute: BNU

data_processing:
Clean data were filtered and quality controlled from raw data, then alignment step was performed.
Gene expression analysis
Differential expression analysis
Gene Ontology enrichment analysis and pathway enrichment analysis
Assembly: mm10
Supplementary files format and content: tab-delimited file includes FPKM values of gene for each sample

source_name: Alveolar bronchus

growth_protocol: Sorted neutrophils were collected in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: No treatment

value: Alveolar bronchus

value: sorted neutrophils

tag: infection

value: Intranasal PR8 infection of mice


title: Amel_adult_antenna_control_worker_biol rep2

value: antennae


title: Input of ChIPseq for Ctcf and Adnp in wt mES cells, replicate 2 [Adnp-3FV5_Input_r2]

data_processing:
Barcoded samples were pooled and sequenced on an Illumina HiSeq 2500 instrument.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within ).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Kaaij et al, 2019.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/6

tag: cell line_clone

value: clone 6F


title: Neutrophils in the bronchoalveolar lavage fluid (BALF) of WT mice,control,  biological replicate 2

value: Control


title: Neutrophils in the bronchoalveolar lavage fluid (BALF) of WT mice,control, biological replicate 1


title: A.baumannii_Saureus_CFCM_Rep4

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

data_processing:
mapping: bowtie2 2.4.1, default parameters
read trimming: trimmomatic 0.36, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
differential gene expression analysis: R 3.6.3 and DESeq2 1.26, default parameters
Assembly: ASM1467273v1, ASM1346v1
Supplementary files format and content: Table S2 RNAseq Ab in USA300 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S3 Main RNAseq pathways Ab.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S4 RNAseq Sa in A118 CFCM.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: Table S5 Main RNAseq pathways Sa.xlsx; Excel Table, Differential Gene Expression data
Supplementary files format and content: ReadCounts_AbA118_in_CFCM_and_TSB.ods
Supplementary files format and content: ReadCounts_SaUSA_in_CFCM_and_TSB.ods

organism: Acinetobacter baumannii A118

source_name: bacteria

extract_protocol:
peqGOLD Total RNA Kit, VWR Peqlab, Darmstadt, Germany
llumina® Stranded Total RNA Prep Kit

value: bacteria

tag: treatment

value: Saureus CFCM Medium


title: Control Biopsy 2

description: Control Biopsy 2

value: Lung

tag: disease state

value: fibrotic lung disease

value: Biopsy


title: ChIPseq for Ctcf in wt mES cells, replicate 2 [Adnp-3FV5_CTCF_ChIP_r2]

tag: chip antibody

value: anti Ctcf (Cell Signaling, #2899)


title: Control Biopsy 1

description: Control Biopsy 1

value: Epithelium, mesenchyme


title: A.baumannii_Saureus_CFCM_Rep2


title: IDH-mutant Recombinant ASPN replicate 2 [252_ASPN2]

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCh38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: hg38
Supplementary files format and content: Counts

source_name: brain

growth_protocol: GBM cells were maintained in DMEM:F12 with B27 minus vitamin A, and supplemented with FGF, EGF and heparin plus antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy Microkit.
Library was prepared using TruSeq Stranded RNA (100ng) +Ribozero Gold.
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end, 2X100bp on Novaseq SP

treatment_protocol: GBM cells were treated with recombinant human ASPORIN (100ng/ml) for 72 hours

value: brain

value: Astrocytoma

value: Tumor

value: IDH-mutant

value: Recombinant ASPN


title: Input of ChIPseq for Ctcf and Adnp in wt mES cells, replicate 1 [Adnp-3FV5_Input_r1]

value: clone 1.2


title: Plasma from HGPS, 194p

value: sodium heparin plasma

value: HGPS


title: A.baumannii_Saureus_CFCM_Rep3


title: neutrophil-GCA-5

city: Guangzhou, China

first: Wangjun

last: Liao

address: Guangzhou Dadao North Road No.1838, Baiyun District

institute: Nanfang Hospital

data_processing:
Raw sequencing data was filtered by Trimmomatic (version 0.36). Low-quality reads were discarded while the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of GRCm38/mm10 from ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/ using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files and Microsoft excel files that include RPKM values and counts reads for all samples

source_name: mouse bone marrow neutrophil

growth_protocol: Mouse bone marrow derived Ly6G+ neutrophils were sorted using EasySep magnetic beads and cultured in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNAs were extracted from mouse neutrophils using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI.
Qualified RNAs were quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210). 2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Bile acids added into culture medium respectively for 24 h of stimulation: TCA 200 μM, GCA 200 μM, Tβ-MCA 10 μM.

value: mouse bone marrow neutrophil

value: WT

value: 200μM GCA for 24 hours

tag: time

value: 24 hours


title: IDH-mutant Recombinant ASPN replicate 1 [252_ASPN1]

city: Los Angeles


title: ChIPseq for Ctcf in wt mES cells, replicate 1 [Adnp-3FV5_CTCF_ChIP_r1]

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/6


title: neutrophil-GCA-4


title: Plasma from HGPS, 230


title: IDH-mutant Control replicate 3 [252_CTL3]

value: CTL


title: neutrophil-GCA-3


title: ChIPseq for Adnp in wt mES cells, replicate 2 [Adnp-3FV5_FLAG_ChIP_r2]

value: clone 6F

value: anti FLAG M2 (Sigma, F1804)


title: Neutrophils in the bronchoalveolar lavage fluid (BALF) of  WT mice,virus, biological replicate1

value: Alveolar bronchus

value: sorted neutrophils

value: Intranasal PR8 infection of mice


title: A.baumannii_control_Rep4

value: bacteria

value: TSB medium


title: neutrophil-TβMCA-5

value: 10μM T[beta]MCA for 24 hours


title: Amel_adult_antenna_control_worker_biol rep1

value: antennae


title: ChIPseq for Adnp in wt mES cells, replicate 1 [Adnp-3FV5_FLAG_ChIP_r1]

value: clone 1.2


title: A.baumannii_control_Rep3


title: EGCG Biopsy 4

description: EGCG Biopsy 4

value: Lung

value: Epithelium, mesenchyme

value: fibrotic lung disease

value: Biopsy

value: EGCG


title: IDH-mutant Control replicate 2 [252_CTL2]

value: brain

value: Astrocytoma

value: Tumor

value: IDH-mutant


title: neutrophil-TβMCA-4

value: mouse bone marrow neutrophil

value: WT

value: 24 hours


title: IDH-mutant Control replicate 1 [252_CTL1]

value: CTL


title: A.baumannii_control_Rep2

value: bacteria

value: TSB medium


title: neutrophil-TβMCA-3

value: 10μM T[beta]MCA for 24 hours


title: FC12738944

city: Rochester

first: Dongmei

state: NY

address: 265 Crittenden Boulevard Cu 420708

department: Clinical and Translational Research

institute: University of Rochester

library_source: other

data_processing:
Norgen uses an Advanced Pipeline for the processing of raw counts and alignment to endogenous genome and annotated transcriptome. We perform initial steps for adapter trimming, QC, filtering and mapping to contaminants. Then, the pipeline maps reads to endogenous and exogenous genomes. The pipeline provides detailed mapping of miRNA, tRNA and piRNA.
Assembly: human endogenous and exogenous genomes
Supplementary files format and content: CSV file include raw counts for each miRNA in each sample

molecule: other

source_name: Plasma

extract_protocol:
Norgen’s RNA isolation and library preparation is based on their patented RNA binding matrix, silicon carbide, which allows us to capture miRNAs without phenol/chloroform and without any bias to GC content. Norgen’s Plasma/Serum Exosome Purification and RNA Isolation Mini Kit (Cat. 58300)
We follow a standard library preparation workflow for all samples (Figure 1). The workflow includes 3' and 5' adapter ligation, followed by reverse transcription and then the indexing PCR. The target band is then excised from the PAGE gel and purified.

value: Plasma

value: W1 Exclusive e-cig user

tag: batch


title: neutrophil-TCA-5

tag: genotype

value: 200μM TCA for 24 hours


title: IDH-wildtype Recombinant ASPN replicate 3 [408_ASPN3]

value: GBM tumor

value: IDH-wildtype

value: Recombinant ASPN


title: FC14975170


title: A.baumannii_control_Rep1


title: A.baumannii_Saureus_CFCM_Rep1

value: Saureus CFCM Medium


title: neutrophil-TCA-4


title: FC12342347


title: IDH-mutant Recombinant ASPN replicate 3 [252_ASPN3]

value: brain

value: Astrocytoma


title: neutrophil-TCA-3


title: neutrophil-PBS-6

value: PBS as control


title: IDH-wildtype Recombinant ASPN replicate 1 [408_ASPN1]

value: Tumor


title: P. cristatum, f/20, Day 16, rep3

city: Selinsgrove

first: Sophie

last: Charvet

state: PA

address: 514 University Avenue

institute: Susquehanna University

description: significanlty increased ingestion of fluorescently labeled bacteria (compared to negative control and to other treatments)

data_processing:
quality check FastQC, Rcorrector, TrimGalore, followed by Kraken to identify and remove prokaryote reads
Assembly: rnaSPAdes - using 3 replicates from each experimental condition. Followed by BLASTn to remove prokaryote transcripts and re-assembly and CD-HIT-EST
Read mapping and counts were performed using Salmon
Assembly: PcrisNIES626_rnaSPAdes.fsa
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Pterosperma cristatum

growth_protocol: P. cristatum cultures (monoprotistan, non-axenic) were grown at 17-18°C, in a 12h day/night cycle under an irradiance of 80 µE m-2 s-1

extract_protocol:
cells were harvested by filtration on 0/8 µm, RNA was extracted using Trizol reagent and the PureLink RNA mini kit  (Invotrogen). 0.2-1.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for polyA selection with a TruSeq library preparation

treatment_protocol:
f/2 medium was prepared according to Guillard (1975), without adding silicate
f/20 medium was obtained with a 10x dilution of f/2 in artificial seawater.

value: aged culture in f/20 medium, nutrient depleted (ND)

tag: format


title: IDH-wildtype Control replicate 3 [408_CTL3]


title: FC15004636

last: Li


title: neutrophil-PBS-5

value: mouse bone marrow neutrophil

value: WT

value: 24 hours


title: IDH-wildtype Control replicate 2 [408_CTL2]

value: CTL


title: FC13228225


title: FC14969962


title: IDH-wildtype Control replicate 1 [408_CTL1]


title: FC14993247

value: W1 Non-user


title: P. cristatum, f/20, Day 16, rep2

tag: strain


title: IDH-wildtype Recombinant ASPN replicate 2 [408_ASPN2]


title: P. cristatum, f/20, Day 16, rep1


title: neutrophil-PBS-3