title: 198

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description:
level-1.csv
level-2.csv
level-3.csv
level-4.csv
level-5.csv
level-6.csv
level-7.csv
feature-table.biom.tsv

data_processing:
Library strategy: 16S rRNA sequencing
For microbiome data analysis, we first removed adapters and low quality reads (Q<30) from the sequencing reads with Trim Galore (v0.4.4). QIIME2 was used to profile the microbial community. In QIIME2, reads were first denoised and dereplicated with the dada2 algorithm prior to being classified against the SILVA database (v132) with a clustering at 99% sequence identity criterion.
For microbial pathway analysis, KEGG pathway abundances were estimated using the PICRUSt2 software.
Supplementary_files_format_and_content: The taxa abundance data for each level is in .csv format, with each row representing sample ID, each column represents taxa ID.
Supplementary_files_format_and_content: KEGG abundance data is in .tsv format, with each row represents KEGG ID, each column represents sample ID.

organism: mouse gut metagenome

source_name: cecal patch

growth_protocol: A30P α-syn and wild-type mice have been maintained on a C57BL/6 background for over 10 generations.

extract_protocol:
Cecal patch tissue was snap frozen and stored at -80°C until processing for DNA isolation. Frozen cecal patch samples were ground on liquid nitrogen into a fine powder. DNA was then isolated from the tissue powder using the Powersoil DNA isolation kit (Qiagen) according to manufacturer’s protocol and quality was determined by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
The 16S rRNA concentration in each sample was confirmed by qPCR using the forward primer: 5’-TCCTACGGGAGGCAGCAGT, and reverse primer: 5’-GGACTACCAGGGTATCTAATCCTGTT. Cecal patch samples were then processed for sequencing according to the Illumina’s 16S Metagenomic sequencing library protocol (doc. #15044223). Briefly, 16S rRNA was amplified from samples using forward primer: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, and reverse primer: 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC. The 16S rRNA V3-V4 region amplicon (550 bp) was verified by gel electrophoresis. The amplicon was then purified using AMPureXP beads. The purified amplicon was indexed using Nextera XT index kit according to the manufacturer’s protocol. Sample libraries were purified with AMPure XP beads, verified with an Agilent 2100 Bioanalyzer, and quantified with a Qubit dsDNA HS kit on a Qubit 3.0 fluorometer (Thermo Fisher Scientific). Sample libraries were then pooled in equimolar amounts.
The Michigan State University Genomics Core performed pooled library quality and quantification using a combination of the Qubit dsDNA HS kit, Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS and Kapa Illumina Library Quantification qPCR assays. Sequencing was performed on a Illumina MiSeq v3 flow cell, loading a library concentration of 3 pM and a 30% spike-in of the Illumina PhiX control DNA library. Sequencing was performed in a 300 bp paired-end format on an Illumina MiSeq. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.

treatment_protocol: Gut inflammation was induced using dextran sodium sulfate (DSS). Adult wild-type and A30P α-syn mice (3-months of age) were exposed to a chronic DSS protocol that began at DSS concentration of 2.5% and increased to 4% over 4 cycles (+0.5% increment per cycle). One cycle consisted of 5 days of DSS, followed by 2 days of water (DSS: 160110, MP Biomedicals, LLC). The non-DSS colitis groups were administered normal drinking water. Mice were then given a 4-week long recovery period during which they received normal drinking water, followed by tissue harvest. Mice were anesthetized with pentobarbital and transcardially perfused with PBS before tissue collection.

value: Cecal patch

tag: gender

value: Male

tag: treatment

value: DSS


title: COVID-19 Positive samples rep 20

status: Public on Aug 01 2021

type: SRA

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

library_source: transcriptomic

data_processing:
illumina universal adapters and low quality reads were removed using cutadapt 2.8. We removed reads with quality scores less than 20 and discarded reads smaller than 36 bp.
The processed reads were then mapped to the human genome GRCh38 using STAR 2.7.3a with default parameters 88. The STAR index was generated using the GRCh38 genome and annotation gtf file downloaded from ENSEMBL 89. BAM files generated were then sorted according to position using Samtools 1.10 90.
Uniquely aligned reads were counted using HTSeq 93. Genes with read count 0 across all the samples were removed from further analysis.
Differential gene expression analysis was performed using DESeq2_1.24.0 94. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered significantly differentially expressed.
Genome_build: GrCh38
Supplementary_files_format_and_content: count Data from BAM using htseqcount in text file

molecule: total RNA

organism: Homo sapiens

source_name: COVID-19 positive samples

extract_protocol:
Total RNA was extracted from 1ml of VTM using TRIzol reagent (Thermo Fisher Scientific, USA) or TRIzol in combination with Direct-zol RNA Microprep Kits (Zymo, USA) according to the manufacturerâ€™s protocol. RNA was quantified using Qubit RNA HS Assay Kit (Thermo Fisher Scientific, USA) and 1 Âµg total RNA was used for library preparation. Ribosomal RNA was removed using the RiboCop rRNA Depletion Kit (Lexogen, Austria).
RNA-Seq libraries were made using the CORALL Total RNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturerâ€™s protocol. Briefly, rRNA depleted RNA was reverse transcribed using displacement stop primers which contain partial Illumina-compatible P7 sequences. Linkers containing partial Illumina-compatible P5 sequences and Unique Molecular Identifiers were ligated to the 3â€™ end of cDNA fragments. The library was PCR amplified to add the remaining adapter sequences and 12 nucleotide unique indices for multiplexing. Samples were sequenced at PE150 using the Illumina NovaSeq 6000.

tag: subject status

value: COVID-19 Positive

tag: sample type

value: nasopharyngeal or oropharyngeal swabs

tag: molecule subtype

value: ribodepleted RNA


title: COVID-19 Positive samples rep 15


title: MCF7 sgNTR1

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

country: USA

institute: UT MD Anderson Cancer Center

library_source: genomic

data_processing:
Library strategy: PCR amplicon sequencing
For the RNASeq data: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome and GENCODEV25 transcriptome using STAR-2.6.1b with parameters "--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate". Counting reads in features with htseq-count (htseq/0.11.0) with parameters "--stranded reverse --additional-attr gene_name gene_type" (human annotation file: hg38/gencode.v25.primary_assembly.annotation.gff3). The normalization of raw read count and differential expression were done by DESeq2/1.22.2 in R/3.5.1.
For the CRISPRi data: sequencing reads were mapped to the sgRNA library using bowtie/1.2.2 with parameters "bowtie --best --strata -a --norc -m 1  -5 20 -3 30 -S -p 12 sgRNAlibrary prefix.fastq 2>prefix.log|samtools view -Sb -F 4 - |samtools sort -@ 5 -o prefix.bam". The sgRNA read count was obtained using "samtools idxstats". The depleted or enriched genes were called using MAGECK/v 0.5.7 using parameters "mageck test -k PseudoMCF7_readcounts.tsv -t MCF7PSED21R1,MCF7PSED21R2,MCF7PSED21R3 -c MCF7PSED0R1,MCF7PSED0R2,MCF7PS  ED0R3 --norm-method control --gene-lfc-method secondbest -n MCF7D21VD0 --control-sgrna PseudoMCF7_negctrl.lst --norm  counts-to-file --additional-rra-parameters \"--permutation 10000\" 2>MCF7D21VD0.log"
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: read count and differential expression result in Excel file; CRISPRi: read count in text files and MAGECK call result in Excel files.

molecule: genomic DNA

growth_protocol: MCF7-dCas9, MDA-MB-231-dCas9 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hyclone #SH30022.01), supplemented with 10% Fetal Bovine Serum, and 1% penicillin/streptomycin. The authenticated MCF7 and MDA-MB-231 cells were cultured in RPMI-1640 (Hyclone #SH30027.1) supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C.

extract_protocol:
Total genomic DNA was extracted from MCF7 and MDA-MB-231 cells using QIAamp DNA Mini Kit.Total RNA was extracted from MCF7 cells using the RNeasy Mini kit.
Two rounds of PCR were employed to prepare the next-generation-sequencing (NGS)-ready sgRNA libraries with the KAPA HiFi HotStart ReadyMix (Roche # KK2602). The first-round PCR was conduced for 16 cycles, using 40 g of input genomic DNA from each replicate at D0 or D21 as a template. The PCR product of different samples was pooled and 20 l of the mixed product was used as a template for the second-round PCR, which was conducted for 12 cycles to incorporate Illumina barcode sequences. The final PCR product was purified from 2% agarose gel with QIAquick Gel Extraction Kit. Concentration of different libraries was measured using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Thermo # Q32851) on a Qubit Fluorometer (Thermo fisher). Two ug of RNA was used for RNA-seq library construction with TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594).

treatment_protocol: MCF7-dCas9 and MDA-MB-231-dCas9 cell lines were infected with lenti virus containing the sgRNA library

tag: cell line

tag: genotype/variation

value: negative control


title: BDL1

city: HangZhou

first: jingyang

last: qian

address: No. 886, Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
The raw sequencing data from 10X Genomics were aligned and quantified using the CellRanger (10X Genomics) suite (version 3.0.2). The mouse genome mm10 was used as the reference genome and the CellRanger count module was used to map reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx files. Matrix table with raw gene counts for every gene and every cell.

organism: Mus musculus

source_name: Liver, BDL

extract_protocol:
Liver NPCs were isolated from mice according to a two-step collagenase method. In detail, murine livers were perfused in situ via the inferior vana cava with calcium-free Hank’s Balanced Salt Solution (HBSS, Gibco, Cat#14170112) containing 0.2 mg/mL EDTA (Sigma, Cat#E6758), followed by 0.4 mg/mL pronase (Sigma, Cat#P5147-1G) and 0.2% collagenase type II (Worthington, Cat#LS004176) at a perfusion rate of 8 mL/minute. Then livers were surgically removed and cut into small pieces. Tissues were transferred in HBSS containing 0.2% collagenase type II, 0.4 mg/mL pronase and 0.1 mg/mL DNase I (Roche, Cat#10104159001), and then incubated for digestion at 37℃ in a water bath for 20 minutes. DMEM (Mediatech, Cat#10-013-CV) containing 10% serum (FBS, Gibco, Cat#10099-141C) was added at the end of the incubation. Sequentially, hepatocytes removal was achieved by centrifugation for 3 minutes at 50 g. Then cell suspension was filtered using a 40 μm nylon cell strainer (Falcon, Cat#352340). Erythrocytes were lysed by treatment with 3-5 mL ACK lysing buffer (Gibco, Cat#A1049201) for 5 minutes after which PBS (Beyotime Biotec, Cat#C0221A) was added to terminate the lysis. The resulting suspension was subjected to Dead Cell Removal Kit (Miltenyi Biotec, Cat#130090101) to remove dead cells according to the manufacturer’s recommendations. The obtained cell pellet was washed twice and suspended in PBS. Cell viability was assessed by Trypan Blue (Gibco, Cat#15250-061).
Liver NPCs single cell suspensions were loaded onto the 10x Genomics Chromium chip (10x Genomics; Pleasanton, CA, USA) to generate droplets. Then the obtained Gel Beads-in-emulsion (GEMs) were transferred into a PCR tube strip, followed by reverse transcription using ProFlex PCR System (Thermo Fisher, MA, USA). The resulting cDNA was purified and amplified for 12 cycles before cleanup with SPRIselect beads (Beckman, Cat#B23318). Based on the cDNA concentration determined by Qubit (Thermo Fisher, MA, USA), libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Model of alcoholic liver disease was constructed by two weeks of chronic ethanol feeding plus a single binge ethanol feeding. Model of non-alcoholic steatohepatitis was built by a long-term feeding of methionine/choline deficient diet (MCD) containing 45 kcal% fat. Model of liver ischemia-reperfusion injury was established by the surgery that 70% warm hepatic ischemia for 45 min and reperfusion for 24 h. Model of drug-induced liver injury was constructed by once intraperitoneal injection of 300 mg/kg acetaminophen for 24 h. Model of cholestatic liver injury was established by bile duct ligation for 10 days. Subsequently, unbiased scRNA-seq analysis and validation experiments were performed.

tag: disease model

value: Cholestatic liver injury

tag: cell type

value: Liver non-parenchymal cells (NPCs)


title: APAP1

source_name: Liver, APAP

value: Drug-induced liver injury


title: MCF7 sgNTR3


title: 187

tag: genotype

tag: tissue

value: Female

value: Water


title: COVID-19 Positive samples rep 17


title: ALD3

source_name: Liver, ALD

value: Alcoholic liver disease


title: COVID-19 Positive samples rep 13


title: 185


title: BDL2


title: MCF7 sgNTR2


title: 201


title: MCF7 sgMGAT4EP R2

value: MGAT4EP knockdown


title: 178


title: COVID-19 Positive samples rep 14


title: ALD2


title: MCF7 sgMGAT4EP R1


title: 191


title: MCF7 D21R3

tag: time point

value: Day 21

tag: replicate


title: 203


title: MCF7 D21R1


title: 189


title: COVID-19 Positive samples rep 12


title: ALD1


title: COVID-19 Positive samples rep 11


title: MCF7 D0R2

value: Day 0


title: MCF7 D0R3


title: COVID-19 Positive samples rep 10


title: MCF7 D21R2


title: 176


title: MCF7 D0R1


title: CON3

source_name: Liver, control

value: Healthy


title: 175

value: Cecal patch


title: COVID-19 Positive samples rep 9


title: 174


title: CON2


title: CON1


title: Lung lobes cells - Gata_d0_18 [ECS047F4]

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
The bcl2fastq software was used for base calling.Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence, then mapped to Mus musicals transcriptome (GRCm38.p6 version 67) using STAR 2.7.0.
Genome_build: GRCm38.p6 version 67
Supplementary_files_format_and_content: tab-delimited text files include count for each Sample and Matrix table with raw gene counts for every gene and every sample

source_name: Lung lobes cells - Gata_d0

extract_protocol:
RNA extraction dedicated lung lobes were placed in RNAlater (Invitrogen, Carlsbad, CA). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Lung lobes cells

tag: collection point

value: baseline

value: Eosinophil KO

tag: disease state

value: TB infected


title: 177


title: COVID-19 Positive samples rep 7

value: COVID-19 Positive

value: nasopharyngeal or oropharyngeal swabs

value: ribodepleted RNA


title: PT1_siPR_1_Input

city: Chicago

first: Shimeng

last: Liu

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

data_processing:
library strategy: MethylCap-seq
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Sequences were aligned to the hg19 reference genome using Bowtie2. Histone style peak calling, differential binding analysis (getDifferentialPeaksReplicates.pl), and motif analysis were performed using Homer under default settings. Differentilly methylated regions (DMRs) were detected with a fold enrichment over background tag count ≥4 and poisson enrichment p-value over background tag count <0.0001. Differential DNA methylation at select regions was validated through Methylcap followed by qPCR.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are peak files from each individual MethylCap-Seq.

source_name: primary uterine LM cells_siCtrl

growth_protocol: Primary LM cells were isolated from fresh LM tissue and cultured within two passages. Primary cells were cultured in DMEM/F12 1:1 (GIBCO/BRL, 11320-082) containing 10% (vol/vol) FBS in a humidified atmosphere in 5% (vol/vol) CO2 at 37 °C.

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, 69504) and fragmented to 300-500bp using Covaris M220. Methylated DNA fragments were captured using the MethylCap Kit (Diagenode, C02020010).
Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710).

treatment_protocol: LM cells were transfected with two different PGR siRNAs (Dharmacon, D-003433-03-0010 and D-003433-01-0010) or control siRNA (D-001810-10-05) for 72 hours, and then stimulated with progesterone agonist R5020 (10-7M) for 24 hours before harvesting.

tag: subject id

value: Patient 1

value: Primary uterine leiomyoma cells

tag: passage

value: primary P1 cells

value: siPGR

value: Input DNA


title: COVID-19 Positive samples rep 8


title: PT2_siPR_1_Input

value: Patient 2


title: Lung lobes cells - Gata_d0_16 [ECS047F2]

tag: treatment


title: 173

tag: gender

value: Female

value: DSS


title: 172


title: Lung lobes cells - Gata_d0_17 [ECS047F3]


title: COVID-19 Positive samples rep 6

tag: subject status

tag: sample type


title: PT1_siCtrl_Input

source_name: primary uterine LM cells_siPGR

value: siCtrl

tag: molecule subtype


title: 171

value: Cecal patch


title: 170


title: PT2_siCtrl_Input

tag: genotype/variation


title: COVID-19 Positive samples rep 4


title: PT2_siPR_1_IP

value: MethylCap DNA


title: 169


title: Lung lobes cells - B6WT_d0_14 [ECS047D5]

source_name: Lung lobes cells - B6WT_d0

value: Lung lobes cells

value: baseline

value: Wild Type


title: PT2_siCtrl_IP


title: COVID-19 Positive samples rep 2

value: COVID-19 Positive


title: 168

value: Water


title: PT1_siPR_1_IP


title: Lung lobes cells - B6WT_d0_12 [ECS047D3]

value: TB infected


title: COVID-19 Positive samples rep 3

value: nasopharyngeal or oropharyngeal swabs

value: ribodepleted RNA


title: 162


title: COVID-19 Positive samples rep 5


title: PT1_siCtrl_IP

value: Patient 1

value: Primary uterine leiomyoma cells

value: primary P1 cells


title: Lung lobes cells - Gata_d0_15 [ECS047F1]

value: Eosinophil KO


title: PT2_siPGR-2

data_processing:
Libraries were sequenced under 50bp single-end sequencing format. Sequences were aligned to the hg19 reference genome using STAR. Raw count files were generated using HTSeq based on Ensembl Release 75 annotation. Differentilly expressed genes were detected using DESeq2 following the cutoff FDR-adjusted P<0.05. Key differentially expressed genes between siCtrl and siPGRs were validated through qPCR.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are HTSeq raw count files from each RNA-Seq sample

source_name: Primary uterine leiomyoma cells

extract_protocol:
Total RNA was extracted using Qiagen RNeasy RNA mini kit (Qiagen, 74104).
Next-generation sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (NEB, #7775).

tag: tissue preparation

value: Primary P1 cells

tag: patient id

value: Patient 2

value: uterine leiomyoma

tag: knockdown


title: COVID-19 Negative samples rep 5

source_name: COVID-19 negative controls

value: COVID-19 Negative


title: Lung lobes cells - B6WT_d0_10 [ECS047D1]

tag: cell type


title: COVID-19 Negative samples rep 4


title: PT3_siPGR-2

value: Patient 3


title: Lung lobes cells - B6WT_d0_13 [ECS047D4]

value: Lung lobes cells


title: 160

tag: genotype

tag: tissue

value: Cecal patch

value: Male


title: Lung lobes cells - B6WT_d93_8 [ECS047C4]

source_name: Lung lobes cells - B6WT_d93

tag: strain

value: day 90

value: Wild Type


title: COVID-19 Positive samples rep 1

value: COVID-19 Positive


title: COVID-19 Negative samples rep 3

value: nasopharyngeal or oropharyngeal swabs


title: Lung lobes cells - B6WT_d0_11 [ECS047D2]

tag: collection point

value: baseline

value: TB infected


title: PT1_siPGR-2

value: Patient 1


title: 161

value: DSS


title: 158

value: Water


title: Lung lobes cells - B6WT_d93_9 [ECS047C5]

tag: disease state


title: 157


title: PT2_siPGR-1

value: Primary P1 cells


title: COVID-19 Negative samples rep 1

value: ribodepleted RNA


title: CVB Stem Cell Cytoplasm Fraction Replicate 2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
CVB_iPSC_cyto_rep2
deseq2_normalized_counts.txt

data_processing:
Fastq files were trimmed for adapters using cutadapt
Trimmed reads were aligned to the human genome build hg19 using STAR aligner
seCLIP : Binding region peaks were identified based on read pileup densities (Clipper)
seCLIP : Reproducible peaks were identified by comparing replicate read pileups along binding regions
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts text file
wiggle files
peak text files

source_name: stem cells

growth_protocol: stem cells were grown in feeder-free conditions using mTeSR on matrigel-coated plates. Stem cell-derived motor neurons were generated using a widely published dual-smad inhibition-based protocol, including intermittent expansion of motor neuron progenitor (MNP) cells in DMEM/F12 medium supplemented with N2 and B27 supplements plus ascorbic acid, CHIR99021, DMH1, SB431542, retinoic acid, purmorphamine and valproic acid.

extract_protocol:
for ceFRA-seq samples, RNA was extracted using either Trizol (total, nuclear, insoluble) or Trizol LS (cytoplasm) following manufacturer's standard protocol
libraries for ceFRA-seq were generated using Illumina Truseq stranded mRNA library prep kits, eCLIP libraries using in-house seCLIP library prep protocol
RNAseq (polyA), seCLIP-seq

treatment_protocol: "stress" samples were treated with puromuycin at 10ug/ml for 24h. "recovery" samples were treated with puromycin at 10ug/ml for 24h, followed by a washout and allowed to recover in puromycin-free medium for 72h

value: hiPSCs

tag: cell line

value: CV-B hiPSC line

value: Untreated

tag: fraction

value: Cytoplasm


title: PT3_siPGR-1

value: Patient 3

value: uterine leiomyoma


title: 159

value: Cecal patch

value: Male

tag: treatment


title: COVID-19 Negative samples rep 2

value: COVID-19 Negative


title: PT1_siPGR-1


title: PT3_siCtrl

value: siCtrl


title: Lung lobes cells - Gata_d93_3 [ECS047A3]

source_name: Lung lobes cells - Gata_d93

value: Lung lobes cells

value: day 90

value: Eosinophil KO


title: Lung lobes cells - Gata_d93_4 [ECS047A5]

value: TB infected


title: Lung lobes cells - Gata_d93_5 [ECS047A6]


title: Lung lobes cells - B6WT_d93_6 [ECS047C2]

value: Wild Type


title: PT1_siCtrl

value: Primary P1 cells

value: Patient 1


title: PT2_siCtrl

value: Patient 2


title: Lung lobes cells - B6WT_d93_7 [ECS047C3]


title: 153

tag: gender

value: Female

value: Water


title: 155

value: DSS


title: 154


title: 156


title: 151


title: PT5_PGR_ChIP_Input

description: Chromatin input from PT5_PGR_ChIP sample

data_processing:
Libraries were sequenced under 75bp single-end sequencing format. Adapters were trimmed using cutadapt. Sequences were aligned to the hg19 reference genome using Bowtie2. Factor style peak calling, differential binding analysis (getDifferentialPeaksReplicates.pl), overlapping region identifications (mergePeaks -d 100) and motif analysis were performed using Homer under default settings.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are peak files from each individual PGR ChIP-Seq

extract_protocol:
0.2-0.5g of fresh frozen LM tissues (patient number = 5) were used for ChIP-Seq using the SimpleChIP Kit (Cell Signaling Technology, #9005). PGR antibody was purchased from Santa Cruz (#sc-7208X).
Next-generation sequencing libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8502) and KAPA Single-Indexed Adapter Kit (KAPA Biosystems, KK8710).

value: Fresh frozen tissue

value: Patient 5

tag: chip antibody

value: none (input)


title: PT4_PGR_ChIP_Input

description: Chromatin input from PT4_PGR_ChIP sample

value: Patient 4

value: uterine leiomyoma


title: 149

value: Cecal patch

value: Male


title: Lung lobes cells - Gata_d93_1 [ECS047A1]

value: Lung lobes cells

value: day 90


title: mESC_small_RNA_WT_treatment.alkaline_fragmentation.rep2

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality and adapter-containing reads were trimmed from Spike-In oligos raw sequencing data using trim-galore package in single-end mode. Reads shorter than 50 bp were removed.
We used fastx_collapser in FASTX-toolkit to collapse identical sequences in a fastq file into a single sequence, which was used to remove duplicated  reads from PCR amplification.
The modified reads were aligned to the reference genome (hg19 for HeLa cells or mm10 for mESC) using bowtie2 (v2.3.3.1)(small RNA) and tophat2(PolyA+ RNA) under default parameters.
Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9). Sorted bam files were subsequently filtered to get the unique mapped reads using samtools view(-q 5). Rnaseqmut was used to identify mutations under the “-t -s 2 -m 2” parameters.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: txt/mutation list

source_name: Mouse embryonic stem cells

growth_protocol: ESC culture using ES medium: DMEM, 15% fetal bovine serum, nucleosides (100x), 1 mM l-glutamine, 1% nonessential amino acid stock, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 mM CHIR99021 and 1 mM PD0325901.

extract_protocol:
200-300 ng of cellular small RNA (size < 200 nt) was fragmented into 40-50 nt under alkaline condition(5 ul NaHCO3 buffer pH=9.2) and purified by Oligo Clean & Concentrator. Then RNA was subjected to demethylation treatment with 1.0 µL of engineered AlkB (D135S, 10 mg/mL) with the reported recipe, followed by purification using Oligo Clean & Concentrator. Chromatin associated RNA purified from cells was added RNase free water to 45 ul and 5 ul NaHCO3 buffer (pH = 9.2) was added and the mixture was incubated at 95 °C for 10 min and then transferred into ice. It was purified by Oligo Clean & Concentrator.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: HeLa cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 ˚C with 5% CO2

value: Wild type

value: Mouse embryonic stem cells

tag: rna population

value: small RNA


title: PT3_PGR_ChIP_Input

description: Chromatin input from PT3_PGR_ChIP sample

value: Patient 3


title: 148


title: mESC_small_RNA_WT_treatment.alkaline_fragmentation.rep1


title: 147


title: Lung lobes cells - Gata_d93_2 [ECS047A2]

value: Eosinophil KO

value: TB infected


title: PT2_PGR_ChIP_Input

description: Chromatin input from PT2_PGR_ChIP sample

value: Patient 2


title: PT1_PGR_ChIP_Input

description: Chromatin input from PT1_PGR_ChIP sample

value: Patient 1


title: PT5_PGR_ChIP

description: PGR ChIP DNA

value: Fresh frozen tissue

value: anti-PGR Santa Cruz (sc-7208X)


title: HeLa_small_RNA_shALKBH1_treatment.alkaline_fragmentation.rep2

source_name: HeLa cells

value: ALKBH1 knockdown

value: HeLa cells


title: HeLa_small_RNA_shALKBH1_Input.alkaline_fragmentation


title: HeLa_small_RNA_control_treatment.alkaline_fragmentation.rep1


title: mESC_small_RNA_WT_Input.alkaline_fragmentation


title: HeLa_small_RNA_control_Input.alkaline_fragmentation


title: HeLa_caRNA_shALKBH1_treatment.alkaline_fragmentation.rep1

value: chromatin associated RNA


title: mESC_small_RNA_ALKBH1KO_treatment.alkaline_fragmentation.rep2


title: HeLa_small_RNA_shALKBH1_treatment.alkaline_fragmentation.rep1


title: HeLa_small_RNA_control_treatment.alkaline_fragmentation.rep2


title: mESC_small_RNA_ALKBH1KO_treatment.alkaline_fragmentation.rep1


title: 145

source_name: cecal patch

value: Cecal patch

value: DSS


title: 146

value: Male

value: Water


title: HeLa_caRNA_shALKBH1_treatment.alkaline_fragmentation.rep2


title: HeLa_caRNA_control_treatment.alkaline_fragmentation.rep2

value: Wild type


title: mESC_small_RNA_ALKBH1KO_Input.alkaline_fragmentation

value: Mouse embryonic stem cells


title: 143


title: PT3_PGR_ChIP

description: PGR ChIP DNA

value: uterine leiomyoma


title: mESC_caRNA_WT_treatment.alkaline_fragmentation.rep2


title: 144


title: HeLa_caRNA_shALKBH1_Input.alkaline_fragmentation


title: 142


title: mESC_caRNA_WT_treatment.alkaline_fragmentation.rep1


title: mESC_caRNA_WT_Input.alkaline_fragmentation


title: HeLa_caRNA_control_treatment.alkaline_fragmentation.rep1


title: HeLa_small_RNA_shAlkBH1_treated.rep2

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality and adapter-containing reads were trimmed from Spike-In oligos raw sequencing data using trim-galore package in single-end mode. Reads shorter than 50 bp were removed.
We used fastx_collapser in FASTX-toolkit to collapse identical sequences in a fastq file into a single sequence, which was used to remove duplicated  reads from PCR amplification.
The modified reads were aligned to the reference genome (hg19 for HeLa cells or mm10 for mESC) using bowtie2 (v2.3.3.1)(small RNA) and tophat2(PolyA+ RNA) under default parameters.
Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9). Sorted bam files were subsequently filtered to get the unique mapped reads using samtools view(-q 5). Rnaseqmut was used to identify mutations under the “-t -s 2 -m 2” parameters.
Genome_build: hg19
Supplementary_files_format_and_content: txt/mutation list
Library strategy: f5C-seq

growth_protocol: HeLa cells were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 ˚C with 5% CO2

extract_protocol:
200-300 ng of cellular small RNA (size < 200 nt) was fragmented into 40-50 nt using RNA Fragmentation Reagent (AM8740, Invitrogen) following the manufacturer’s protocol and purified by Oligo Clean & Concentrator. Then RNA was subjected to demethylation treatment with 1.0 µL of engineered AlkB (D135S, 10 mg/mL) with the reported recipe, followed by purification using Oligo Clean & Concentrator.
Libraries were prepared according to Illumina's instructions

value: AlkBH1 knockdown

value: HeLa

value: small RNA


title: ML3325 (MG1655 pKVS45-GapR1-76-3xFLAG), in exponential phase, induced with aTc, replicate 2

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

description: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and then fixed by the addition of 10 mM sodium phosphate [pH 7.6] and 1% formaldehyde (final concentrations). ChIP was then performed as previously reported (Guo et al, 2018).

data_processing:
Reads were aligned to Escherichia coli MG1655 (NC_000913.2) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655

extract_protocol:
ChIP was performed as previously reported (Guo et al, 2018).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.

tag: growth stage

value: exponential phase

tag: media

value: LB + 25 ng/µL aTc

tag: treatment protocol

value: Cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr.


title: mESC_caRNA_ALKBH1KO_Input.alkaline_fragmentation


title: 10X_1-4mHet_1

city: Boston

first: Jeong

middle: H

last: Yun

state: MA

address: 181 Longwood Ave

institute: BRIGHAM AND WOMEN'S HOSPITAL

data_processing:
For 10X Chromium libraries, sequencing output was demultiplexed by Cell Ranger (version 2.0.0), for inDrops libraries, sequencing output was demultiplexed by dropTag-dropEst pipeline
Cells were filtered if UMI counts were over 3000 or less than 200, as well as mitochondrial percent over 15%
Each library count matrices was processed with variance stabilizing transformation (SCTransform workflow) in Seurat v3.1.4. All library count matrices were integrated using a reference library (4m Het-2) that had the highest sequencing depth per cell using 30 dimensions.
Cell clusters were identified by inputing 40 principal components for UMAP embedding and cluster identification using Leiden algorithm with resolution 1.5 in Seurat v3.1.4.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object with meta data  (Seurat R object retrieve by readRDS)

source_name: lung

extract_protocol:
For harvesting, mice were euthanized by CO2 asphyxiation followed by exsanguination.  Lungs were perfused with chilled PBS via the right heart.  For lung cells isolation without enrichment (15 out of 18 samples), dispase (50 U-mL) was instilled into lungs, which were dissected and minced on ice into approximately 1 mm3 cubes.  Lungs were digested using collagenase-dispase for 30 mins at 37°C, then passed through a 40 um cell strainer.  Cells were centrifuged at 300 RCF for 5 mins, then incubated with RBC lysis buffer.  Cells were stained with trypan blue for viability assessment which showed greater than 85% viability with this method. The single cell suspension was sorted by FACS for DAPI-negative viable cells using MoFlo Astrios EQ.
For enriched CD45- lung cells (4mHet-3, 4mWt-2, 8mHet-3), lungs were digested using a mouse lung isolation kit with gentleMACS dissociator (Miltenyi), then were passed through a 40 um cell strainer. After centrifugation at 300 RCF for 5 mins, cells were incubated with RBC lysis buffer. Cells were then stained with DAPI, DRAQ5 (abcam) and CD45-PE Ab (BioLegend), and selected for DAPI negative, DRAQ5 positive and CD45 negative cells using On-chip Sort cell sorter (On-chip Biotechnologies)(Watanabe et al., 2014).
single cell RNA libraries were prepared for sequencing using 10X Genomics Chromium V2 protocols and inDrops

value: lung

tag: age

value: 4 months

value: Hhip+--

tag: cell type enrichement


title: ML3325 (MG1655 pKVS45-GapR1-76-3xFLAG), in exponential phase, induced with aTc, replicate 1

growth_protocol: Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and then fixed by the addition of 10 mM sodium phosphate [pH 7.6] and 1% formaldehyde (final concentrations). ChIP was then performed as previously reported (Guo et al, 2018).


title: PT2_PGR_ChIP

description: PGR ChIP DNA

tag: tissue preparation

value: Fresh frozen tissue

tag: patient id

value: Patient 2

tag: cell type

value: anti-PGR Santa Cruz (sc-7208X)


title: PT4_PGR_ChIP

description: PGR ChIP DNA

value: Patient 4


title: HeLa_caRNA_control_Input.alkaline_fragmentation

tag: genotype

value: HeLa cells

value: chromatin associated RNA


title: 141

tag: tissue

value: Cecal patch

value: Male

value: Water


title: 138


title: Tumour_combi

city: Oxford

first: James

last: McAuliffe

state: Oxfordshire

address: Old Road Campus Research Building, Roosevelt Drive

department: Ludwig Institute for Cancer Research,

country: United Kingdom

institute: University of Oxford

data_processing:
Raw data was proceed using cellranger pipeline (10X genomics) version 2.2.0 as described by the manufacturer
The command cellranger mkfastq was first used to demultiplex the Illumina sequencer's base call files (BCLs) into FASTQ files.
The command cellranger count was then used to perform alignment, filtering, barcode counting, UMI counting and to generate expression matrix files.
UMI count matrices for the filtered set of barcodes (representing cells) were used as determined by cellranger. Expression matrices output by cellranger are in Matrix Market Exchange format (.mtx). The gene and cell barcode name files that accompany the mtx files are provided as tsv files (.tsv) for each sample.
Further downstream data analysis was performed using R package Seurat v3.1.4
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression matrices output by cellranger are in Matrix Market Exchange format (.mtx). The gene and cell barcode name files that accompany the mtx files are provided as tsv files (.tsv) for each sample.

source_name: 15V4T3 tumour

growth_protocol: 15V4T3 cells were expanded in culture and then implanted subcutaneously in the right-flanks of DBA/2 mice. Tumour growth was monitored upon the formation of palpable tumours. Mice were sacrificed and spleens/tumours excised 25 days following tumour implantation.

extract_protocol:
Spleens/tumours were collected from mice 25 days following tumour implantation. Following treatment, spleens and tumours were collected, processed to single-cell suspension via mechanical and enzymatic disruption of tissue, and samples from the same experimental group pooled together for each tissue type. P1A-35-43-specific CD8+ T-cells were then isolated from spleens and tumours by MHC-class I multimer staining and FACS sorting and resuspended in PBS-FCS. Cells were then loaded onto the 10X Genomics Chromium system as per manufacturer's instructions. Library construction was performed according to the 10X Chromium Single Cell 5' Reagent Kit
Single cell libraries were constructed with the Single Cell 5' Reagent Kit from 10X genomics

treatment_protocol: Tumour-bearing mice were treated with either ChAdOx/MVA P1A vaccine alone (10^7 IU / 10^6 PFU doses 1-week apart), or with ChAdOx/MVA P1A vaccine (10^7 IU / 10^6 PFU doses 1-week apart) + anti-PD-1 inhibitor (3-doses of 100μg 3-days apart) combination.

tag: strain

value: 15V4T3 tumour

value: Vaccine + anti-PD-1

value: WT


title: 10X_1-4mWt_1

value: Hhip+-+


title: BL1

city: Shanghai

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

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

data_processing: FPKM

source_name: Human fetal scleral fibroblasts

extract_protocol: none provided by the submitter

value: Human fetal scleral fibroblasts


title: mESC_caRNA_ALKBH1KO_treatment.alkaline_fragmentation.rep1

value: Mouse embryonic stem cells


title: HeLa_small_RNA_control_Input

value: wild type

tag: cell line

value: HeLa

value: small RNA


title: PT1_PGR_ChIP

description: PGR ChIP DNA

value: Fresh frozen tissue

value: Patient 1

value: uterine leiomyoma


title: 140


title: 10X_1-4mHet_2

value: lung

value: 4 months

value: Hhip+--


title: HeLa_small_RNA_shAlkBH1_treated.rep1

value: AlkBH1 knockdown


title: NC1


title: mESC_caRNA_ALKBH1KO_treatment.alkaline_fragmentation.rep2

value: chromatin associated RNA


title: mRNA-Seq si-circCpsf6-2

city: Shenzhen

first: Changrui

last: Tie

institute: Shenzhen Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: N2A cells

growth_protocol: Neuro2A cells were cultured in DMEM supplemented with 10% fetal bovine serum, and 1% Penicillin/Streptomycin.

extract_protocol:
Different Total RNAs of N2A cells  were harvested using Trizol reagent. TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of mRNA sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For siRNA, si-NC and si-circCpsf6 were mixed with RNA iMAX Reagent and their final concentration was 100nM.

value: neuroblast

value: brain

tag: disease

value: neuroblastoma


title: HeLa_small_RNA_control_treated.rep2


title: HeLa_small_RNA_shAlkBH1_Input


title: mRNA-Seq si-circCpsf6-3


title: 10X_1-11mWt_2

value: 11 months

value: Hhip+-+


title: mRNA-Seq si-circCpsf6-1


title: mRNA-Seq si-NC-1


title: Mus astrocyte KO TGF-β (1)

city: Baltimore

first: Horea

last: Rus

state: MD

address: 655 W Baltimore St

department: Department of Neurology

institute: University of Maryland, School of Medicine

data_processing:
Analysis was performed with the VIPER pipeline on the BIOWUlf Server at the NIH, using the following parameters:
Alignemnts were performed with the STAR aligner for unstranded libraries
gene level counts were determined using cufflinks
samples were batch corrected
differential expression was performed using the DESeq protocol, and siginificantly regulated genes were considered with at least 1.5 x fold change and p<0.05 FDR
Genome_build: mm10
Supplementary_files_format_and_content: File Name
Supplementary_files_format_and_content: Tatomir_2022_Raw_counts.csv: raw gene counts of sequencing reads - all samples
Supplementary_files_format_and_content: Tatomir_2022_Cufflinks_Genecounts.csv: normalized gene counts - all samples
Supplementary_files_format_and_content: WTCTvsTGF.deseq.annot.csv: differentially expressed genes in WT astrocytes, treated or not treated with TGFbeta
Supplementary_files_format_and_content: KOCTvsTGF.deseq.annot.csv: differentially expressed genes in KO astrocytes, treated or not treated with TGFbeta

source_name: Primary neonatal astrocytes

growth_protocol: The brains were minced and sequentially passed through nylon meshes. The resulting cell suspensions were plated onto 75-cm2 plates in DMEM/Ham’s F-12 medium containing 10% fetal bovine serum (FBS) for 2 weeks. Oligodendrocyte precursor cells and neurons were separated from the astrocyte monolayer by shaking overnight at 200 rpm on a rotary shaker. The non-adherent cell suspension was discarded, and adherent astrocytes were then maintained in DMEM/Ham’s F-12 medium containing 10% FBS

extract_protocol:
Total RNA from mouse astrocytes was purified using an RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions. For each genotype and treatment, two biological replicates were analyzed, and a total amount of 1 µg of RNA was used for each sample
Unstranded Library construction according to Genewiz protocol

treatment_protocol: Astrocytes were serum-starved overnight prior to stimulation with 10 ng/ml TGF-β (Gemini Bio, West Sacramento, CA) for 24 h

value: Primary neonatal brain astrocytes

value: RGC-32 knock-out

value: post natal day 1

tag: treatment

value: treated with TGF-Beta for 24h


title: HeLa_small_RNA_control_treated.rep1

value: wild type

value: HeLa

value: small RNA


title: 10X_1-11mHet_2

value: lung


title: HeLa_mRNA_control_treated.rep2

molecule: polyA RNA

extract_protocol:
500 ng polyA+ RNA purified from HeLa cells was added RNA water to 45 ul and 5 ul NaHCO3 buffer (pH = 9.2) was added and the mixture was incubated at 95 °C for 10 min and then transferred into ice. It was purified by Oligo Clean & Concentrator.
Libraries were prepared according to Illumina's instructions

value: PolyA+ mRNA


title: 10X_1-11mHet_1

value: Hhip+--


title: Spleen_combi

source_name: Spleen

value: Spleen

value: Vaccine + anti-PD-1

value: WT


title: 10X_1-11mWt_1


title: HeLa_mRNA_shAlkBH1_Input

value: AlkBH1 knockdown


title: Tumour_vac

value: 15V4T3 tumour

value: Vaccine


title: RNA-seq: KO_Effector_rep3

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Mapped reads were counted using htseq-count version 0.9.1 and Ensembl GRCm38.90 gtf files with the following arguments: ‘-m union -s no -f bam’
Genome_build: mm10
Supplementary_files_format_and_content: tab seperated values with one column per sample and one row per gene containing raw counts

source_name: KO Effector CD8

extract_protocol:
CD8 T cell subsets were flow cytometrically sorted and resuspended in Trizol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of Flow cytometrically purified cells were resuspended in Trizol (Ambion Life Technologies) and total RNA was extracted according to the manufacturer’s protocol. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Only RNA samples having an RNA Integrity Number (RIN) > 8 were subjected to library generation.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: Mice were injected i.v. with 10000 CFU L. monocytogenes (N4). 7 days after injected spleen was isolated and sorted by flow cytometry.

value: Spleen CD44+ CD62L-, 7 days after infection with L. monocytogenes


title: mRNA-Seq si-NC-2

value: neuroblast

value: brain

value: neuroblastoma


title: RNA-seq: KO_Effector_rep4


title: HeLa_mRNA_control_Input


title: mRNA-Seq si-NC-3


title: Mus astrocyte KO Control (1)

value: Primary neonatal brain astrocytes

value: RGC-32 knock-out

value: post natal day 1

value: untreated


title: RNA-seq: WT_Effector_rep3

source_name: WT Effector CD8


title: RNA-seq: WT_Effector_rep4


title: HeLa_mRNA_shAlkBH1_treated.rep1

value: HeLa


title: mESC_small_RNA_AlkBH1KO_treated.rep2

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality and adapter-containing reads were trimmed from Spike-In oligos raw sequencing data using trim-galore package in single-end mode. Reads shorter than 50 bp were removed.
We used fastx_collapser in FASTX-toolkit to collapse identical sequences in a fastq file into a single sequence, which was used to remove duplicated  reads from PCR amplification.
The modified reads were aligned to the reference genome (hg19 for HeLa cells or mm10 for mESC) using bowtie2 (v2.3.3.1)(small RNA) and tophat2(PolyA+ RNA) under default parameters.
Mapped sam files were subsequently converted and sorted to bam files using samtools sort (v1.9). Sorted bam files were subsequently filtered to get the unique mapped reads using samtools view(-q 5). Rnaseqmut was used to identify mutations under the “-t -s 2 -m 2” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: txt/mutation list
Library strategy: f5C-seq

value: embryonic stem cells

value: small RNA


title: Mus astrocyte KO TGF-β (2)

value: treated with TGF-Beta for 24h


title: HeLa_mRNA_shAlkBH1_treated.rep2

value: PolyA+ mRNA


title: Mus astrocyte KO Control (2)


title: RNA-seq: KO_Effector_rep1


title: Mus astrocyte WT TGF-β (1)

value: wild type


title: Spleen_vac

value: Spleen

value: WT


title: MM Patient 2

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
The sequenced data were de-multiplexed using mkfastq (cellranger 10X genomics, v3.0.2) to generate fastq files
After de-multiplexing, the reads were aligned to the human reference genome (GRCh38; 10x cellranger reference GRCh38 v3.0.0)
Feature-barcode matrices were generated using the cellranger count, and then aggregated by cellranger aggr using default parameters.
Genome_build: 10x cellranger reference GRCh38 v3.0.0
Supplementary_files_format_and_content: barcode, feature, matrix files for each sample

source_name: Bone marrow

extract_protocol:
Sorted single cells were processed using the 10X Chromium Single cell 3’ Reagent Kit v3 (10X genomics) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Natural killer (NK) cells

value: multiple myeloma


title: RNA-seq: WT_Effector_rep2

value: Spleen CD44+ CD62L-, 7 days after infection with L. monocytogenes


title: mESC_small_RNA_WT_treated.rep1


title: HeLa_mRNA_control_treated.rep1


title: mESC_small_RNA_AlkBH1KO_treated.rep1


title: Mus astrocyte WT Control (2)


title: ChIP-seq: H3K79me2_WT_Effector_rep3

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM version 0.7.15-r1140 with the following argument: ‘-M’
Duplicates were marked with picard’s MarkDuplicates version 2.12 with the following arguments:’VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=false’
Reads with a mapping quality less than 37 or any bits in the flag set to 1804 were excluded with Samtools version 1.3
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage version 3.0.1 from deepTools with the following arguments: ‘-of bigwig --binSize 25 --normalizeUsing RPGC --ignoreForNormalization chrM --effectiveGenomeSize 2652783500’; Scores represents reads per genomic content.

extract_protocol:
Flow cytometrically purified cells were cross-linked, and chromatin lysates were prepared. Histone-DNA complexes were isolated with antibodies.
Library preparation was done using KAPA LTP Library preparation kit using the manufacturer’s protocol with slight modifications. Briefly, after end-repair and A-tailing adaptor were ligated followed by SPRI clean-up. Libraries were amplified by PCR and fragments between 250-450 bp were selected using AMPure XP beads (Beckman Coultier). The libraries were analyzed for size and quantity of DNAs on a 2100 Bioanalyzer using a High Sensitivity DNA Kit (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

value: Spleen CD44+ CD62L-, 7 days after infection with L. monocytogenes. Mouse LckCre+/-;Dot1Lwt/wt

value: H3K79me2 (Milipore 04-835)


title: RNA-seq: KO_Effector_rep2


title: mESC_mRNA_WT_treated.rep1

extract_protocol:
500 ng polyA+ RNA purified from mES cells was added RNA water to 45 ul and 5 ul NaHCO3 buffer (pH = 9.2) was added and the mixture was incubated at 95 °C for 10 min and then transferred into ice. It was purified by Oligo Clean & Concentrator.
Libraries were prepared according to Illumina's instructions


title: WT

city: Jinan

first: Ruonan

last: Duan

address: 44# Wen Hua Xi Road

institute: Shandong University

data_processing:
We first processed 10X genomics raw data by the Cell Ranger Single-Cell Software Suite, including using cellranger  mkfastq to demultiplexes raw base call files into FASTQ files and then using cellranger count to preform alignment, filtering, barcode  counting, and UMI counting.
The reads were aligned to the hg19 reference genome using a pre-built annotation package download  from the 10X Genomics website.
Then we mapped UMIs to genes, followed by removing low-quality cells.
Data was first normalized by ‘‘NormalizeData’’ function with setting normalization method as ‘‘LogNormalize’’.
We then restricted the corrected expression matrix to the subsets of highly variable genes (HVGs), and then centered and scaled  values before performing dimension reduction and clustering on them.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix, barcodes and genes  table for every gene and every cells

source_name: cortices and hippocampus

extract_protocol:
Tissues were processed by using the Adult Brain Dissociation Kit (Miltenyi Biotec).
Library preparation was performed according to the instructions of the 10X Chromium single-cell kit.

value: 2-month old

value: cortices and hippocampus


title: mESC_small_RNA_WT_Input


title: Smek1-/-


title: RNA-seq: WT_Effector_rep1


title: mESC_mRNA_WT_treated.rep2


title: mESC_mRNA_WT_Input


title: Mus astrocyte WT Control (1)

value: Primary neonatal brain astrocytes

value: post natal day 1

value: untreated


title: MM Patient 1


title: CRIS-sc rep3

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
CRIS.sc.3
SNHG1 knockout (single cell)

data_processing:
Adaptor trimming by cutadapt
Alignment by STAR
Gene count by HTSeq-count
TMM Normalization by edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene read counts and CPM values.

growth_protocol: Human neuroblastoma cell lines SK-N-BE(2)C cells were routinely generated by re-plating day 4 (typically 1 × 106 cells into a 10 cm dish) and cultured in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum. Cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Neuroblastoma cell line SK-N-BE(2)C was cultured in 6-well plate for 2 days. Next, the cells were homogenized in 500 μl TRIzol® Reagent and cell lysates were collected. Then 100 μl chloroform was added and cellular RNAs were extracted. The solution was centrifuged at 12,000 xg for 15 minutes. Supernatant was collected into new eppendorf with same volume of 100% EtOH and centrifuged at 13,000 xg for 1 minute. RNA wash buffer (400 μl) was added to the column and centrifuged at 13,000 xg for 1 minute. DNase I (5 μl) and DNA Digestion Buffer (75 μl) was added into column and kept at RT for 15 minutes. Direct-zol RNA Prewash (400 μl) was added to the column and centrifuged at 13,000 xg for 1 minute. Washing step was repeated again. After next, RNA Wash Buffer (700 μl) was added to the column and centrifuged at 13,000 xg for 2.5 minutes. Flow-through was discarded and centrifuged at 13,000 xg for 2.5 minutes again. Then, column was transferred into new RNase-free tube. To elute RNA, RNase-free water (20 μl) was added directly into the column matrix and centrifuged at 13,000 xg for 1 minute. RNA concentration was determined by NanoDrop ND-1000 (NanoDrop Technologies, Montchanin, DE, USA) and RNA quality was checked by 1% agarose gel electrophoresis.
Libraries were constructed uing SureSelect Strand Specific RNA Library kit according to the manufacturers

treatment_protocol: On the day of transfection, cells were optimal at 80% confluency. Constructs carried Cas9 and dual sgRNAs and pSurrogate reporters were introduced into cells by co-transfection using Lipofectamine 3000 transfection reagent (Invitrogen) according to the manufactures’ protocol. At 16-24 hours post-transfection, the culture medium was replaced with fresh medium containing puromycin to remove non-transfected cells. After 3-7 days puromycin selection, single cell clones were isolated by fluorescence cell sorting into 96-well plates and incubated for 1-2 weeks. The sorted clones were then expanded and cultured in 10 cm dish.

value: SNHG1 gRNA

value: neuroblastoma


title: mESC_small_RNA_WT_treated.rep2

value: embryonic stem cells

value: small RNA


title: CRIS-sc rep1

description:
CRIS.sc.1
SNHG1 knockout (single cell)


title: ChIP-seq: H3K79me2_WT_Effector_rep1


title: mESC_small_RNA_AlkBH1KO_Input


title: ChIP-seq: H3K79me2_WT_Effector_rep2

value: Spleen CD44+ CD62L-, 7 days after infection with L. monocytogenes. Mouse LckCre-/-;Dot1Lwt/wt


title: CRIS-clone rep1

description:
CRIS.clone.1
SNHG1 knockout (clone)


title: MM Patient 3


title: CRIS-clone rep2

description:
CRIS.clone.2
SNHG1 knockout (clone)


title: mESC_mRNA_AlkBH1KO_Input

value: PolyA+ mRNA


title: Control rep3

description:
Control.3
wildtype

value: non-targeting control gRNA


title: TCL rep1

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over mouse RefSeq genes using htseq-count
Normalization was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESeq2 output

source_name: BM DCs

extract_protocol:
BM cell were isolated from mice then sorted by flow cytometry sorter according to DCs markers
Inhouse poly A based RNA seq

value: bone arrow

value: dendritic cells

tag: disease state

value: TCL (murine CLL)


title: mESC_mRNA_AlkBH1KO_treated.rep2


title: TCL rep2


title: TCL rep3


title: CRIS-clone rep3

description:
CRIS.clone.3
SNHG1 knockout (clone)


title: 10X_2-8mHet_3

value: lung

value: 8 months

value: Hhip+--


title: 10X_2-4mWt_2

value: 4 months

value: Hhip+-+


title: WT rep1

value: wild type


title: CRIS-sc rep2

description:
CRIS.sc.2
SNHG1 knockout (single cell)


title: RNAPII-ChIA-PET(RNaseA + 400μg/ml)

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: nuclear chromatin

data_processing:
Library strategy: ChIA-PET
RICh-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: RICh-PET:Tab-delimited file documenting the genomic coodinates of DNA and RNA of each interaction PET with RNA strand information; ChIA-PET: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET clusters.

organism:
Drosophila melanogaster
Homo sapiens

growth_protocol: S2 was cultured following manufacture’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 500 bp by sonication. The anti-RNAPII monoclonal antibody 8WG16 (Biolegend, 920102) was used to enrich RNAPII-bound chromatin fragments, respectively.
The DNA fragments in the streptavidin beads-bound chromatin for Standard RICh-PET  or antibody beads-bound chromatin for RNAPII RICh-PET were end-repaired using T4 polymerase (Promega) in mixture (70 µl 10× T4 polymerase buffer, 7 µl 10mM dNTP, 3.5 µl RI, 612.3 µl Nuclease-free water, with 7.2 µl of T4 polymerase), washed with RICh-PET Wash Buffer (10 mM Tris.HCl pH 7.0, 10 mM Tris.HCl pH 8.0, 10 mM EDTA, 50 mM NaCl) three times. The RNA fragments were linked to RNA linker for first-strand cDNA synthesis using the Superscript III First Strand Synthesis System (Thermo Fisher Scientific). In more details, 1 µg of biotinylated and barcoded RNA linker R1 (tube 1) and R2 (tube 2) containing a flanking MmeI site were added to two tubes containing cDNA synthesis mixture (20 µl RNA liker, 20 µl dNTP, 80 µl 5× RT buffer, 20 µl 0.1 M DTT, 20 µl RI, 220 µl Nuclease-free water) and incubated at 65 °C for 5 min (Alternative, incubated at 42 °C for 5 min when performing RNAPII RICh-PET), then placed on ice for at least 1 min, and added 20 µl superScriptIII RT, and incubated for 10 min at 25 °C on Intelli-Mixer (Program F1, 10rpm), followed by 30 min at 50 °C (Alternative, 1 hour at 37 °C when performing RNAPII RICh-PET). The RNA linker ligated chromatin was washed with Wash Buffer three times, then incubated with 1 µg of DNA linker D1 (tube 1) and D2 (tube 2) respectively in the ligation mixture (15 µl DNA linker, 140 µl 5× T4 DNA ligase buffer with PEG, 3.5 µl RI, 536.5 µl Nuclease free water) by using 5 µl of T4 DNA ligase at 16 °C for overnight. The linker-added DNA fragments were washed with Wash Buffer three times and then phosphorylated with 14 µl of T4 polynucleotide kinase (NEB) in PNK master mix buffers (70 µl 10× T4 DNA ligase buffer, 3.5 µl RI in 612.5 µl Nuclease-free water). The samples from two tubes were washed with Wash Buffer three times and then were mixed and followed by proximity ligation with 34 µl of T4 DNA ligase in reaction buffer (1,000 µl 10× T4 DNA ligase buffer, 50 µl RI, 8,916 µl Nuclease-free water) overnight at 16 °C. After washing with Wash Buffer three times, the chromatin DNA fragments with linkers were subjected to second-strand cDNA synthesis with a Superscript Double-stranded cDNA Synthesis Kit (Thermo Fisher Scientific) and chromatin mixing with second-strand cDNA mixture (333 µl Nuclease-free water, 90 µl 5× second-strand reaction buffer, 9 µl 10 mM dNTP mix, 3 µl E.coli DNA ligase, 12 µl E.coli DNA Polymerase I, 3 µl E.coli RNase H) were incubated at 16 °C for 2 hours; then 6 µl of T4 DNA polymerase were added and continued to be incubated at 16 °C for 5 min. Crosslinks in the DNA/RNA/protein complexes were then reversed by incubation at 65 °C overnight with 0.5% SDS (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific), and the cDNA-DNA fragments were purified by phenol/chloroform isopropanol precipitation. The purified cDNA-DNA was then digested by 1 µl of MmeI (NEB) in buffer (5 µl 10× NE Buffer 4, 5 µl Half linker non-Biotinylated to quench excess MmeI, 5 µl 10× SAM) for 2 hours at 37 °C to release the [cDNA tag]-[RNA linker]-[DNA linker]-[DNA tag] Paired-End-Tag structure. The biotinylated PETs were then immobilized on streptavidin-conjugated magnetic Dynabeads (Thermo Fisher Scientific, 11206D-10ml) in 50 µl of 2× B&W buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 1 M NaCl), and rotated at room temperature for 45 min. The ends of each PET structure were then ligated to a sequencing adaptor by 1 µl of T4 DNA ligase (Thermo Fisher Scientific, EL0013) in Adaptor ligation buffer (4 µl Adaptor A, 4 µl Adaptor B, 5 µl 10× T4 DNA ligase buffer, 36 µl Nuclease-free water) at 16 °C for overnight with rotation. Then the beads were washed three times with 1× B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). Nick translation was performed by adding 4 µl of E.coli DNA polymerase I solution mixture (38.5 µl Nuclease free water, 10× NEBuffer 2, 2.5 µl 10 mM dNTP) and incubated at room temperature for 2 hours with rotation on the Intelli-Mixer (F8, 30rpm, U = 50, u = 60). Then 10-16 rounds of PCR reactions were performed to amplify the PETs, and the resultant RICh-PET libraries were subjected for sequencing by HiSeq2500 with paired-end reads of 36 bp.

treatment_protocol: Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS.

tag: factor

value: RNAPII


title: RNAPII-ChIA-PET (RNaseA - control)

description: nuclear chromatin


title: WT rep3


title: mESC_mRNA_AlkBH1KO_treated.rep1

tag: rna population


title: Control rep1

description:
Control.1
wildtype


title: H23_rep1

type: RNA

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

description: gene expression data from NCI-H23

hyb_protocol: Following fragmentation, 2.3 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: The raw data of the array were collected as CEL files and analysed using the Transcriptome Analysis Console (TAC 4.1) software. The gene expression was analysed with the Gene Level SST-RMA summarization method.

label: biotin

source_name: KRAS G12C NCI-H23 cell line

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA(Gene Chip WT PLUS Reagent kit, Affymetrix)

growth_protocol: The H23 and H23ARC11 cell line were maintained in a humidified atmosphere of 5% CO2 at 37 ℃ in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: Trizol extraction of total RNA and DNase treatment were performed according to the manufacturer's instructions

value: Lung

value: Adenocarcinoma; Non-small cell lung cancer


title: H23ARC11_rep1

description: gene expression data from NCI-H23ARC11

source_name: resistance clone of sotorasib-sensitive KRAS G12C NCI-H23 cells


title: WT rep2


title: H23ARC11_rep2

description: gene expression data from NCI-H23ARC11


title: 10X_2-4mHet_3


title: Anther of which floral buds diameter greater than 1.6cm of female flower 1

status: Public on Jul 31 2021

city: nanning

first: tianfeng

last: liu

address: Xixiangtang Street

institute: guangxi university

data_processing:
The samples were sequenced using a BGISEQ-500 Analyzer (BGI Genomics, Shenzhen, China).
Clean reads were assembled by using Trinit.
Tgicl was used to cluster the transcripts to obtain Unigene
Clean reads of each sample were compared to Unigene using Bowtie2 software.
The fragments per Kilobase of transcript per Million mapped reads (FPKM) were calculated was calculated by RSEM.
Supplementary_files_format_and_content: Microsoft Office Excel files include FPKM values for each Sample.
Supplementary_files_format_and_content: fasta files include the sequence and length of genes.

organism: Handeliodendron bodinieri

source_name: Flower

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent according to the manufacturer’s protocol (Invitrogen).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligationoftheadapter.Theproducts arethenpurifiedandenrichedwithPCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays andstepwisesequencingusingCombinationalProbe-AnchorSynthesis SequencingMethod.

tag: Sex

value: female

tag: anther development stage

value: stage 8-9 of anther development

value: anthers


title: Control rep2

description:
Control.2
wildtype

value: neuroblastoma


title: Anther of which floral buds diameter between 1.3~1.6cm of male flower 2

value: male

value: stage 6-7 of anther development


title: Anther of which floral buds diameter between 1.3~1.6cm of female flower 2


title: Anther of which floral buds diameter greater than 1.6cm of male flower 1


title: Anther of which floral buds diameter greater than 1.6cm of female flower 2


title: Anther of which floral buds diameter between 1.3~1.6cm of female flower 1


title: Floral buds diameter greater than 1.6cm of female flower 1

value: floral buds


title: Anther of which floral buds diameter greater than 1.6cm of male flower 3


title: H23_rep2

description: gene expression data from NCI-H23


title: Anther of which floral buds diameter between 1.3~1.6cm of female flower 3


title: Floral buds diameter greater than 1.6cm of female flower 3


title: Floral buds diameter less than 1.3cm of female flower 2

value: stage 3-5 of anther development


title: Anther of which floral buds diameter between 1.3~1.6cm of male flower 1


title: Floral buds diameter between 1.3~1.6cm of male flower 3


title: Floral buds diameter between 1.3~1.6cm of male flower 2


title: Floral buds diameter between 1.3~1.6cm of female flower 3


title: Floral buds diameter between 1.3~1.6cm of female flower 1


title: Floral buds diameter between 1.3~1.6cm of female flower 2


title: Floral buds diameter between 1.3~1.6cm of male flower 1


title: Floral buds diameter less than 1.3cm of male flower 1


title: Floral buds diameter less than 1.3cm of male flower 3


title: IAA-rep-1

status: Public on Jul 23 2021

city: Worcester

first: Paul

middle: D.

last: Kaufman

address: 364 Plantation St.

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
aligned to human primary genome hg38, with star_2.5.3a, annotated with GENECODE GRCh38.p12 annotation release 29
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2
Differential expression (DE) analysis was performed with  DESeq2_1.20.0
Genome_build: hg38
Supplementary_files_format_and_content: Excel, TPM normalized expression values

source_name: HCT116 cells with degron-tagged Ki-67

growth_protocol: HCT116-Ki-67-mAC-AID cells were cultured in DMEM (Gibco) cat#11995065, with 1% penicillin/streptomycin. Cells were incubated in 37 °C, 5% CO2, and 95% humidity. For each biological replicate sample, 1 x 10e6 cells were seeded into each of three 35 mm dishes and grown for 2 days.

extract_protocol:
Media was removed, 0.7 ml Qiazol (Qiagen) was added to each dish and the lysate was collected into Qiashredder tubes (Qiagen) and centrifuged at 12,000 x g for 30 seconds for homogenization. Total RNA was extracted using RNeasy kits (Qiagen) as recommended by the manufacturer. Total RNA concentrations were measured using Qubit reagents (Invitrogen).
mRNA was enriched on oligo-dT beads, and reverse transcribed and sequenced using a PE150 protocol with Illumina reagents at the Novogene corporation.

treatment_protocol: Cells were then either untreated or treated with 0.5 mM indole acetic acid for 24 hours.

value: 0.5 mM indole acetic acid


title: Control-rep-1


title: Anther of which floral buds diameter between 1.3~1.6cm of male flower 3


title: Floral buds diameter less than 1.3cm of female flower 3


title: Floral buds diameter greater than 1.6cm of male flower 1


title: Floral buds diameter greater than 1.6cm of male flower 2


title: Floral buds diameter less than 1.3cm of female flower 1


title: WT_DRIPc_S_rep1

status: Public on Jul 22 2021

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: RNA moiety from RNA:DNA hybrids

data_processing:
library strategy: DNA-RNA immunoprecipitation strand-specific (DRIPc-seq)
Sequenced paired-end reads subjected to quality control pipeline using the FASTQ Toolkit V.1.0.0 software (Illumina) and then mapped to the Saccharomyces cerevisiae reference genome sacCer3 using the Rsubread V 2.0.1 software package with unique=TRUE parameter.  Coverage profiling was performed using bamCoverage from deepTools and RPKM normalisation method was applied. In order to compare properly the samples treated or not with RNH1, we applied a scale factor to RNH-treated samples based on the ratio between the uniquely mapped reads and the total reads of each sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YPAD media at 30ºC with shaking to mid-log phase. Cultures were synchronized at G1 with α-factor and collected for G1 experiments. S phase experiments were collected after G1 release, when the cultures reached S mid-log phase.

extract_protocol:
Genomic DNA was extracted by spheroplasting and isopropanol precipitation. Purified DNA was digested by a cocktail of restriction enzymes (HindIII, EcorI, XbaI, SspI, BsrGI) and then immunoprecipitated using S9.6 antibody. After that, samples were treated with DNase I and RNA was purified.
NEBNext ultra II Directional RNA Library prep kit for Illumina

treatment_protocol: cell cultures were treated with Auxin 1 mM and α-factor simultaneously. After G1 release, auxin 1 mM was added again to the media.

tag: strain background


title: WT_DRIPc_S_rep2

description: RNA moiety from RNA:DNA hybrids


title: Floral buds diameter greater than 1.6cm of male flower 3


title: Anther of which floral buds diameter greater than 1.6cm of male flower 2


title: hpr1_DRIPc_S_rep2

description: RNA moiety from RNA:DNA hybrids

value: YMK612 MATa ura3-3::ADH1-AtTIR1-9myc (URA3) RAD5 bar1-delta hpr1::hpr1-aid (hphB)


title: Control-rep-2


title: IAA-rep-2


title: hpr1_DRIPc_G1

growth_protocol: Yeast strains were grown in YPAD media at 30ºC with shaking to mid-log phase. Cultures were synchronized at G1 with α-factor and collected for G1 experiments. S phase experiments were collected after G1 release, when the cultures reached S mid-log phase


title: MD01-005_NP_H1N1_3

status: Public on Jul 21 2021

first: Kellie

middle: Nicole

last: Smith

address: 1650 Orleans Street, CRB1, 4M

institute: Johns Hopkins University

description: bulk TCR-seq

data_processing:
Library strategy: TCR-seq
Mixcr software used to align and extract information on TCR or immunoglobulin repertoire
Genome_build: hsa
Supplementary_files_format_and_content: tab-delimited text files include clonotype information for each sample

source_name: peripheral blood

growth_protocol: We used the MANAFEST (Mutation Associated NeoAntigen Functional Expansion of Specific T-cells) assay to evaluate T cell responsiveness to MANA and viral antigens. Briefly, pools of MHC class I-restricted CMV, EBV, and flu peptide epitopes (CEFX, jpt Peptide Technologies), pools representing the matrix protein and nucleoprotein from H1N1 and H3N2 (jpt Peptide Technologies), and putative neoantigenic peptides defined by the ImmunoSelect-R pipeline (jpt Peptide Technologies) were each used to stimulate 250,000 T cells in vitro for 10 days as previously described. Briefly, on day 0, T cells were isolated from peripheral blood mononuclear cells (PBMC) by negative selection (EasySep; STEMCELL Technologies). The T cell–negative fraction was co-cultured with an equal number of selected T cells in culture medium (IMDM/5% human serum with 50 μg/mL gentamicin) with 1 μg/mL relevant neoantigenic peptide, 1 μg/mL of an MHC class I-restricted CMV, EBV, and flu peptide epitope pool (CEFX, jpt Peptide Technologies), 1 μg/mL of pools representing the matrix protein and nucleoprotein from H1N1 and H3N2 (jpt Peptide Technologies), or no peptide (to use as a reference for non-specific/background clonotypic expansion). On day 3, half the medium was replaced with fresh medium containing cytokines for a final concentration of 50 IU/ml IL-2 (Chiron), 25 ng/ml IL-7 (Miltenyi), and 25 ng/ml IL-15 (PeproTech). On day 7, half the medium was replaced with fresh culture medium containing cytokines for a final concentration of 100 IU/mL IL-2 and 25 ng/mL IL-7 and IL-15. On day 10, cells were harvested, washed twice with PBS, and the CD8+ fraction was isolated using a CD8+ negative enrichment kit (EasySep; STEMCELL Technologies).

extract_protocol:
DNA was extracted from each CD8-enriched culture condition using the Qiamp micro-DNA kit according to the manufacturer’s instructions
TCR libraries were prepared for sequencing using standard Illumina protocols

tag: patientid

value: peripheral blood lymphocytes

tag: type of antigen tested

value: Viral pool (Influenza)

tag: gene epitope derived from

tag: epitope tested

value: Viral (Influenza, NP_H1N1)

tag: cells sequenced

value: CD8+ T cells (CDR3)

tag: culture condition

value: 10 day co-culture


title: sen1_DRIPc_S_rep1_RH

description: RNA moiety from RNA:DNA hybrids

extract_protocol:
Genomic DNA was extracted by spheroplasting and isopropanol precipitation. Purified DNA was digested by a cocktail of restriction enzymes (HindIII, EcorI, XbaI, SspI, BsrGI) and then treated with RnaseH. Immunoprecipitation was performed with S9.6 antibody. After that, samples were treated with DNase I and RNA was purified.
NEBNext ultra II Directional RNA Library prep kit for Illumina

tag: genotype

value: YMK612 MATa ura3-3::ADH1-AtTIR1-9myc (URA3) RAD5 bar1{delta} sen1::sen1-aid (hphB)


title: MD01-005_NP_H3N2_3

description: bulk TCR-seq

tag: cell type

value: Viral (Influenza, NP_H3N2)


title: MD01-005_NP_H3N2_1

description: bulk TCR-seq


title: WT_DRIPc_G1

tag: strain


title: sen1_DRIPc_S_rep2

description: RNA moiety from RNA:DNA hybrids


title: Mus astrocyte WT TGF-β (2)

value: Primary neonatal brain astrocytes

value: wild type

tag: age

value: post natal day 1

value: treated with TGF-Beta for 24h


title: Floral buds diameter less than 1.3cm of male flower 2

value: male

tag: tissue


title: sen1_DRIPc_S_rep1

description: RNA moiety from RNA:DNA hybrids


title: MD01-005_NP_H3N2_2

description: bulk TCR-seq


title: hpr1_DRIPc_S_rep1_RH

description: RNA moiety from RNA:DNA hybrids


title: WT_DRIPc_S_rep1_RH

description: RNA moiety from RNA:DNA hybrids


title: hpr1_DRIPc_S_rep1

description: RNA moiety from RNA:DNA hybrids


title: MD01-005_NP_H1N1_2

description: bulk TCR-seq


title: MD01-005_NP_H1N1_1

description: bulk TCR-seq


title: MD01-005_MP1_H1N1_3

description: bulk TCR-seq

value: Viral (Influenza, MP1_H1N1)


title: MD01-005_MP1_H3N2_3

description: bulk TCR-seq

value: Viral (Influenza, MP1_H3N2)


title: NY016-025_NoPep

description: bulk TCR-seq


title: MD01-005_MP1_H1N1_1

description: bulk TCR-seq


title: MD01-005_MP1_H3N2_2

description: bulk TCR-seq


title: NY016-025_6

description: bulk TCR-seq

value: MANA

value: TLFQIIYDNLR


title: NY016-025_7

description: bulk TCR-seq

value: CLASLHPR


title: MD01-005_MP1_H3N2_1

description: bulk TCR-seq

value: peripheral blood lymphocytes


title: NY016-025_5

description: bulk TCR-seq

value: VQNAVQWLR


title: NY016-025_8

description: bulk TCR-seq

value: RSLGCLASLH


title: NY016-025_CEF

description: bulk TCR-seq

value: Viral pool (CMV, EBV, Influenza A)

value: CD8+ T cells (CDR3)


title: MD01-005_HIV

description: bulk TCR-seq

value: Viral (HIV)

value: 10 day co-culture


title: MD01-005_MP1_H1N1_2

description: bulk TCR-seq

value: Viral pool (Influenza)


title: NY016-025_9

description: bulk TCR-seq

value: SHPRH

value: KLLHEYWMSLR


title: NY016-025_16

description: bulk TCR-seq

value: MEESNNSTL


title: NY016-025_1

description: bulk TCR-seq

value: AVQWLRPK


title: NY016-025_2

description: bulk TCR-seq

value: NEB

value: HVMPDTPDILK


title: NY016-014_6

description: bulk TCR-seq

value: MANA

value: YLDSIVFLEDL


title: NY016-025_3

description: bulk TCR-seq

value: KVMYILFY


title: NY016-014_5

description: bulk TCR-seq

value: peripheral blood lymphocytes

value: FLEDLSPL


title: NY016-025_4

description: bulk TCR-seq

value: VQNAVQWLRPK


title: NY016-025_17

description: bulk TCR-seq

value: MEESNNSTLFI


title: Anther of which floral buds diameter greater than 1.6cm of female flower 3

value: female

value: stage 8-9 of anther development

value: anthers


title: NY016-014_32

description: bulk TCR-seq

value: MAFSPAVDV

value: CD8+ T cells (CDR3)

value: 10 day co-culture


title: NY016-014_3

description: bulk TCR-seq

value: HMAFSPAV


title: NY016-025_14

description: bulk TCR-seq

value: SHPRH

value: LHEYWMSL


title: NY016-014_25

description: bulk TCR-seq

value: MSYDNNLF


title: NY016-025_13

description: bulk TCR-seq

value: MANA

value: EVQNAVQWL


title: NY016-025_15

description: bulk TCR-seq

value: YKLLHEYWMSL


title: NY016-014_24

description: bulk TCR-seq

value: peripheral blood lymphocytes

value: YPDYLDSIVFL


title: NY016-014_22

description: bulk TCR-seq

value: MPLVHMAFSPA


title: NY016-025_12

description: bulk TCR-seq

value: QVNKVMYILFY


title: NY016-025_11

description: bulk TCR-seq

value: EVKEEDEPF


title: NY016-025_10

description: bulk TCR-seq

value: LLHEYWMSLR


title: NY016-014_21

description: bulk TCR-seq

value: MPLVHMAF


title: NY016-014_No_Pep

description: bulk TCR-seq


title: NY016-014_2

description: bulk TCR-seq

value: LLADATVELSL


title: NY016-014_CEF

description: bulk TCR-seq

value: Viral pool (CMV, EBV, Influenza A)

value: CD8+ T cells (CDR3)


title: NY016-014_7

description: bulk TCR-seq

value: FLEDLSPLEA

value: 10 day co-culture


title: NY016-014_9

description: bulk TCR-seq

value: TLIDVPKV


title: NY016-014_31

description: bulk TCR-seq


title: NY016-014_14

description: bulk TCR-seq

value: MSYDNNLFIK


title: NY016-007_5

description: bulk TCR-seq

value: MANA

value: SON

value: LRNGALTSPIV


title: NY016-014_12

description: bulk TCR-seq

value: peripheral blood lymphocytes

value: VTMACINLASK


title: NY016-007_CEF

description: bulk TCR-seq


title: NY016-014_8

description: bulk TCR-seq

value: LLLHGAEPKL


title: NY016-007_6

description: bulk TCR-seq

value: LARASPAL


title: NY016-014_4

description: bulk TCR-seq

value: YLDSIVFL


title: NY016-007_15

description: bulk TCR-seq

value: QASLARASPA


title: NY016-014_13

description: bulk TCR-seq

value: TMACINLASK


title: NY016-007_16

description: bulk TCR-seq

value: LARASPALA


title: NY016-007_13

description: bulk TCR-seq

value: SLARASPA


title: NY016-007_NoPep

description: bulk TCR-seq

value: CD8+ T cells (CDR3)


title: NY016-014_23

description: bulk TCR-seq

value: YPDYLDSIVF


title: NY016-007_9

description: bulk TCR-seq

value: SAITSKVSTV

value: 10 day co-culture


title: NY016-014_11

description: bulk TCR-seq

value: LSKDIMFHFK


title: NY016-007_12

description: bulk TCR-seq

value: MANA

value: ASLARASPA


title: Floral buds diameter greater than 1.6cm of female flower 2

value: female

value: stage 8-9 of anther development

value: floral buds


title: NY016-007_7

description: bulk TCR-seq

value: peripheral blood lymphocytes

value: SLARASPAL


title: NY016-007_8

description: bulk TCR-seq

value: LRSLTFSLV


title: NY016-007_1

description: bulk TCR-seq

value: SON

value: LTSPIVCF


title: MD043-011_NP_H1N1_3

description: bulk TCR-seq

value: Viral pool (Influenza)

value: Viral (Influenza, NP_H1N1)


title: NY016-014_16

description: bulk TCR-seq

value: VTLIDVPK

value: CD8+ T cells (CDR3)


title: NY016-007_4

description: bulk TCR-seq

value: VLRNGALTSPI


title: MD043-011_MP1_H3N2_3

description: bulk TCR-seq

value: Viral (Influenza, MP1_H3N2)

value: 10 day co-culture


title: MD043-011_MP1_H3N2_1

description: bulk TCR-seq


title: NY016-007_3

description: bulk TCR-seq

value: MANA

value: LRNGALTSPI


title: MD043-011_MP1_H1N1_2

description: bulk TCR-seq

value: Viral (Influenza, MP1_H1N1)


title: MD01-004_NP_H3N2_3

description: bulk TCR-seq

value: Viral (Influenza, NP_H3N2)


title: NY016-007_17

description: bulk TCR-seq

value: KLRSLTFSLV


title: MD01-004_NP_H3N2_2

description: bulk TCR-seq

value: peripheral blood lymphocytes


title: NY016-007_2

description: bulk TCR-seq

value: LARASPALASL


title: NY016-007_14

description: bulk TCR-seq

value: ASLARASPAL


title: NY016-014_1

description: bulk TCR-seq

value: LLADATVEL


title: MD043-011_NP_H3N2_1

description: bulk TCR-seq


title: MD043-011_NP_H3N2_2

description: bulk TCR-seq


title: MD01-004_MP1_H3N2_3

description: bulk TCR-seq


title: MD01-004_NP_H1N1_1

description: bulk TCR-seq


title: NY016-007_11

description: bulk TCR-seq

value: SAITSKVSTV


title: NY016-007_10

description: bulk TCR-seq

value: AITSKVSTV


title: MD043-011_NP_H3N2_3

description: bulk TCR-seq

value: Viral pool (Influenza)


title: MD01-004_MP1_H3N2_2

description: bulk TCR-seq


title: MD043-011_NP_H1N1_1

description: bulk TCR-seq

value: Viral (Influenza, NP_H1N1)


title: MD043-011_NP_H1N1_2

description: bulk TCR-seq

value: CD8+ T cells (CDR3)


title: MD043-011_MP1_H3N2_2

description: bulk TCR-seq


title: MD01-004_MP1_H1N1_1

description: bulk TCR-seq


title: MD043-011_MP1_H1N1_3

description: bulk TCR-seq


title: HFD_3

status: Public on Jul 06 2021

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Zentrum Munich

description:
Polyadenylated RNA's
processed data file: adata_raw.h5
processed data file: adata_processed.h5

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization and batch correction of crypt samples the scanpy python package v.1.0.4 and anndata v0.5.10 and a python implementation of Combat were used. For QC, filtering and normalization of villi samples the scanpy python package v.1.4.4 and anndata v0.7.1 were used. Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/2021_Aliluev_Tritschler_gut_HFD
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format. File contains raw or preprocessed and annotated count data for all experiments.

source_name: Single cells of small intestinal crypts

extract_protocol:
Small intestines were removed, washed with cold PBS and villi were scraped off with a glass slide. Villi were scraped off with a glass slide. The remaining tissue was cut into 2-cm pieces, washed several times with cold PBS and incubated in 2 mM EDTA/PBS for 35 min at 4 Â°C. Subsequently, crypts were harvested by rigorous shaking and filtered through a 70-µm mesh to remove villous fragments. For single cell suspension, isolated crypts were incubated with TrypLE (Life technologies, #12605) for 5 min on ice and then 5 min at 37 Â°C and treated with 10 Âµg/ml DNase in crypt complete medium (DMEM/F-12 containing 10 % FCS) for 5 min at 37 Â°C. For flow cytometry, cells were colleced in 1-2ml FACS buffer (2% FCS, 2mM EDTA in PBS) (Sigma-Aldirch, #Y0503) and passed through the 40µm cell strainer caps of FACS tubes. Small intestinal crypt cells were sorted using FACS-Aria III (BD Bioscience) with a 100 Âµm nozzle. For all experiments, single cells were gated according to their FSC-A (front scatter area) and SSC-A (side scatter area). Singlets were gated dependent on the FSC-W (front scatter width) and FSC- H (front scatter height) and dead cells were excluded using the 7-AAD marker (eBioscience, #00-6993-50). To obtain FVF-enriched small intestinal crypt cell samples for single-cell RNA sequencing, we sorted 30,000 FVF+ (FVFlow and FVFhigh) cells followed by sorting 30,000 live crypt cells per sample. Cells were sorted into modified FACS buffer (2 % FCS, 0.02 mM EDTA in PBS).
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.

value: Foxa2 FVF/FVF

value: small intestinal crypts

value: adult

tag: treatment

value: 12 weeks high-fat-high-sugar diet


title: FFPE_ATAC_on_FFPE_kidne_with_25K_nuclei_rep1

status: Public on Jul 02 2021

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Reads were aligned to the mm9 genome/hg19 genome using bowtie2
duplicate reads were removed with Picard
MACS2  was used call narrow peak
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: peak text files

source_name: Kidney

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA with T7-Tn5. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

value: FVBN

value: FFPE


title: FFPE_ATAC_on_FFPE_kidne_with_25K_nuclei_rep2


title: CD_2


title: MD043-011_HIV

description: bulk TCR-seq

value: Viral pool (HIV)

value: Viral (HIV)

value: 10 day co-culture


title: CD_1


title: MD01-004_NP_H1N1_2

description: bulk TCR-seq

value: peripheral blood lymphocytes


title: MD043-011_MP1_H1N1_1

description: bulk TCR-seq

value: Viral (Influenza, MP1_H1N1)


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_10um_rep1


title: MD01-004_MP1_H3N2_1

description: bulk TCR-seq

value: Viral (Influenza, MP1_H3N2)


title: FFPE_ATAC_on_FFPE_kidne_with_500_nuclei_rep2


title: MD01-004_NP_H3N2_1

description: bulk TCR-seq

value: Viral (Influenza, NP_H3N2)


title: MD01-004_MP1_H1N1_3

description: bulk TCR-seq


title: FFPE_ATAC_on_Frozen_kidney_rep1

value: Frozen


title: FFPE_ATAC_on_Frozen_liver_rep1


title: Standard_ATAC_on_FFPE_kidney_rep2


title: Standard_ATAC_on_FFPE_kidney_rep1


title: MD01-004_MP1_H1N1_2

description: bulk TCR-seq

value: Viral pool (Influenza)


title: NY016-014_10

description: bulk TCR-seq

value: MANA

value: TMACINLA


title: FFPE_ATAC_on_Frozen_kidney_rep2


title: FFPE_ATAC_on_FFPE_kidne_with_500_nuclei_rep1


title: FFPE_ATAC_colon5_rep2

status: Public on Jun 30 2021

source_name: colon

value: colon


title: Standard_ATAC_on_frozen_liver_rep1

source_name: Liver

value: frozon


title: MD01-004_NP_H1N1_3

description: bulk TCR-seq

value: Viral (Influenza, NP_H1N1)

value: CD8+ T cells (CDR3)


title: FFPE_ATAC_colon5_rep1


title: Dicer+/+aviD-/- 2

status: Public on Jul 09 2021

city: London

first: Enzo

last: Poirer

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Reads were trimmed to 40bp using Cutadapt (version 0.1.9) and  mapped to the genome of interest using Bowtie (version 1.2.0) with default parameters with one mismatch (-v 1).
Coverage over ZIKV or SARS-CoV-2 genome was determined using mapped 22 bp reads only, using BEDTools's genome CoverageBed function. version 2.27.1
Genome_build: GenBankID: MK105975.1 [ZIKV] ; MT0795851.1 [SARS]
Supplementary_files_format_and_content: Read coverage (per basepair) over the Zika genome (MK105975.1) or SARS genome (MT0779851.1)

source_name: Brain organoids

extract_protocol:
RNA extraction was performed from organoids grinded in 2 ml Eppendorf tube containing 500 ul TRIzol reagent and one Stainless Steel 5 mm bead (Qiagen) using a TissuLyser LT (Qiagen) at 50 oscillations/s for 1 min. 400 ng of RNA was process for next-generation sequencing using the HiSeq 4000 platform (Illumina).
NEBNext_small_RNA

treatment_protocol: Individual Dicer+/+aviD+/+, Dicer+/+aviD—/— and Dicer—/—aviD+/+ brain organoids were infected with ZIKV or SARS, and collected after 4 days

value: Brain organoids

tag: variation

value: Dicer+/+aviD-/-

tag: infection


title: NY016-014_15

description: bulk TCR-seq

value: CENPE

value: KTWKEKTLK


title: FFPE_ATAC_on_FFPE_kidne_with_5K_nuclei_rep1

value: FVBN

value: FFPE


title: CD_3

value: Foxa2 FVF/FVF

value: small intestinal crypts

value: adult


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_10um_rep2


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_5um_rep2


title: MD01-004_HIV

description: bulk TCR-seq

value: peripheral blood lymphocytes

value: Viral pool (HIV)

value: Viral (HIV)

value: 10 day co-culture


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_7um_rep1


title: FFPE_ATAC_on_FFPE_kidne_with_5K_nuclei_rep2


title: FFPE_ATAC_colon2_rep2

value: colon


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_5um_rep1


title: Standard_ATAC_on_frozen_kidney_rep2

value: frozon


title: FFPE_ATAC_on_FFPE_kidne_with_thickness_of_7um_rep2


title: Standard_ATAC_on_FFPE_liver_rep1


title: FFPE_ATAC_colon2_rep1


title: HFD_1

value: 12 weeks high-fat-high-sugar diet


title: HFD_2


title: FFPE_ATAC_colon1_rep2


title: FFPE_ATAC_colon4_rep1


title: FFPE_ATAC_rectum1_rep1

source_name: rectum

value: rectum


title: FFPE_ATAC_rectum1_rep2


title: FFPE_ATAC_on_Frozen_liver_rep2

value: Frozen


title: Dicer-/-aviD+/+ 2

value: Brain organoids

value: Dicer-/-aviD+/+


title: Standard_ATAC_on_FFPE_liver_rep2


title: Omni_ATAC_liver_rep2

source_name: liver

value: liver


title: FFPE_ATAC_liver_rep1

value: FVBN


title: FFPE_ATAC_colon3_rep1

value: FFPE


title: FFPE_ATAC_liver_rep2