title: 1560

value: mild dysplasia


title: 14404_folded_P2_RNA-seq

status: Public on Sep 30 2022

type: SRA

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: LinPOS organoids RNA-seq

library_source: transcriptomic

data_processing:
Illumina 1.9 software used for conventional basecalling.
Reads were trimmed using TrimGalore v0.4.1.
Reads were mapped using STAR v2.5.2a.
Number of reads that map to genomic features is calculated using HTSeq v0.6.0. Reads with a mapping quality less than 10, or those that map to multiple loci or to overlapping gene regions are discarded to avoid ambiguity and false positives.
PCA  plots and heatmaps are based on normalised and rlog transformed counts obtained with DESeq2 version 1.14.1 (R version 3.4.1). Differential Gene Expression Analysis was done using the counted reads and the R package edgeR version 3.16.5 (R version 3.4.1), for the 3 pairwise comparisons.
Genome_build: Ensembl Homo_sapiens.GRCh38 (release 92)
Supplementary_files_format_and_content: A text file (csv format) includes FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Human fetal lung

growth_protocol: Fetal lung tip organoids were cultured in Matrigel  in self-renweing (SN) culture medium.

extract_protocol:
Total RNA was harvested from lung organoids using Rneasy Kit (Quiagen, 74004) and  Illumina TruSeq RNA Sample Prep Kit (Illumina, 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After complete removal of Matrigel, TripLE (Thermo Fisher Scientific, 12605010) were treated to dissociate organoids into single cells.

tag: sample id

tag: developmetal age

value: 19 pcw

tag: passage number

tag: tissue

value: Human fetal lung

tag: cell type

value: LinPOS organoids

value: Folded


title: ZR-75-1_RNAseq

city: Bangkoknoi

first: Somponnat

last: Sampattavanich

state: Bangkok

address: 2 Wanglang Road

department: Department of Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

data_processing:
Transcriptome sequencing was performed using Illumina Hiseq2000 (Illumina, San Diego, CA) with 150x2 paired-end chemistry reads and sequencing at depth 20-25 million reads per sample.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The STAR (v2.5.3a) was used to align reads to human reference genome (hg19 release).
Other pipelines were used including sambamba (v0.6.6) for sorting the BAM files, samtools (v1.6): for indexing the BAM files, fastp (v0.19.4) for the read trimming and QC and subread (v1.6.2) for the gene/isoform quantification.
The expression levels for each gene were normalized to transcripts per million (TPM) to facilitate the comparison of transcript levels among samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

source_name: breast cancer cell lines

growth_protocol: Cell lines were growth at 5% CO2 and 37C in difference base medium with 2 mM L-glutamin from Gibco (The detail are as follows:MCF7 (Eagle), MMNK-1 (Ham-F12), T-47D (RPMI-1640), ZR-75-1 (RPMI-1640)). Then medium were supplemented with 10% FBS (Biochrom) and 1% Penicillin-Streptomycin(Gibco). Culture medium were change every 2-3 days. Then split cell lines at ratio 1:3 to 1:6 using 0.25% trypsin/EDTA (Gibco) when culture reach confluent. All cell lines were tested mycoplasma before perform an experiment.

extract_protocol:
RNA were extracted from cell lines byTrizol reagent (Invitrogen). RNA purification using Ambion RNA isolation kit (Invitrogen) and perform on-column DNA treatement using PureLink DNase set (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: rrid

value: breast cancer cell lines


title: 13393_CS23_P5_RNA-seq

description: Pseudoglandular organoids RNA-seq

value: Pseudoglandular organoids

value: Cystic


title: iR9-CHILP-12-3

city: Guangzhou, China

first: yunqing

last: Lin

address: Building 3, No.188 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Center for Cell Lineage and Atlas (CCLA)

country: China

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

data_processing:
Bcl2fastq (version 2.16.0.10) convert .bcl files into fastq files.
Fastq files were aligned to mm10 genome. *.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Assembly: mm10
Supplementary files format and content: CHILP_TPM_Matrix.txt: Matrix table with TPM value for every gene and every cell.

molecule: polyA RNA

organism: Mus musculus

source_name: common helper innate lymphoid progenitors

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2 (Vazyme, N711).
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme, TD503).

treatment_protocol: The single CHILPs were sorted for RNAseq analysis.

tag: strain


title: SO_8069_KKK-D068_MEK_RNAseq

source_name: cholangiocarcinoma cell lines

growth_protocol: We cultured KKU-055, KKU-156, KKU-213, KKU-214, KKK-D068, KKK-D131, KKK-D138 HuCCT-1 and HuH-28 in DMEM (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). Four of CCA cell lines which are RBE, SSP-25, TFK-1, YSCCC were cultured in RPMI (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). KKU-100 and HuCCA1 were grown in Ham-F12 (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). MMNK-1 were growth in 2 mM L-glutamin from Gibco (Ham-F12) supplemented with 10% FBS (Biochrom) and 1% Penicillin-Streptomycin (Gibco). All cell lines were tested mycoplasma before perform an experiment.

treatment_protocol: 24 hours after plating cell at 80% confluent, we performed drug treatment using inhibitors from Selleckchem Which are Src/Abl inhibitor(Dasatinib) and MEK inhibitor (PD-0325901). All cell lines were individually treated with inhibitors for 24 hours in 0.5%DMSO at a concentration of 10uM.

value: cholangiocarcinoma cell lines

tag: treatment

value: Thai


title: 14387_folded_P5_ATAC-seq

description: LinPOS organoids ATAC-seq

library_source: genomic

data_processing:
Illumina 1.9 software used for conventional basecalling.
Reads were trimmed using TrimGalore (Krueger 2013) v0.4.1.
For mapping the reads to the genome bowtie2 (Langmead and Salzberg 2012) was used  instead of STAR as recommended by the ENCODE pipeline for processing ATACSeq data. The maximum distance between pairs of reads is set to 2000 nucleotide as per the recommandations from ENCODE.
Duplicates was removed using PicardTools (Wysoker, Tibbetts, and Fennell 2013) and peak calling was ran using the MACS2 (Feng et al. 2012) algorithm (version 2.1.1) for peak calling; shift 75/extsize 150/call-summits/keep-dup all
After peak calling, the interesect of the groups were subtracted to generate each group-specific peak file.  The peak files were annotated using ChipSeeker (G. Yu, Wang, and He 2015), annotating peaks with the closest gene that it related to and the type of features (promoter, UTR, exon, intron…) at the peak position.
Genome_build: Ensembl Homo sapiens.GRCh38 (release 92)
Supplementary_files_format_and_content: A bigwig file (.bw format) for each sample

molecule: genomic DNA

extract_protocol:
50,000 cells were harvested from organoids and lysed in lysis buffer. The lysate was treated in 50 μL reactions with Nextera TDE1 transposase (Illumina, 15027865) for 30 min at 37°C. the transposed DNA was purified using Qiagen MinElute PCR Purification Kit
The purified DNA was amplified and indexed using Nextra DNA CD Indexes (Illumina, 20018707)

value: 20 pcw


title: iR9-CHILP-19-3


title: iR9-CHILP-2-3


title: 14404_folded_P2_ATAC-seq

description: LinPOS organoids ATAC-seq


title: 14404_cystic_P1_RNA-seq

description: LinNEG organoids RNA-seq

value: LinNEG organoids


title: iR9-CHILP-10-3


title: iR9-CHILP-15-3


title: 1488

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

data_processing:
Library strategy: 16S rRNA seq
Sequencing data was processed as forward, single-end reads. Forward reads were trimmed to a total length of 210 bases, such that 75% of reads at each base had a PHRED score greater than 25.
Amplicon sequence variants (ASVs) were denoised using the DADA2 denoising algorithm (v2019.1.0)
Taxonomy was assessed in relation to the SILVA reference database (version 132) using BLAST on the QIIME2 software platform
Assembly: SILVA reference database (v.132)
Supplementary files format and content: CSV file containing relative frequencies of each bacterial species identified within each sample (sample ID, Kingdom, Phylum, Class, Order, Family, Genus, Species, Relative Frequency)

source_name: oral swab

extract_protocol:
DNA isolation was performed on Lesion cytology brush samples using the DNeasy Blood & Tissue Kit (QIAGEN, Hilden Germany). An enzymatic lysis buffer preparation was followed by two centrifugation/wash steps with PBS. The pellet was resuspended in PBS with 20 µl proteinase K and 4 µl of RNase A (100 mg/ml), followed by vortex and incubation. Extraction steps were conducted as per the manufacturer’s kit instructions. DNA was eluted using 50 µl nuclease free distilled water and stored at −20 °C.
A custom16S rRNA gene sequencing approach was employed. A single round of PCR (25 cycles) was done using Platinum SuperFi II DNA Polymerase–High-Fidelity PCR Enzyme for pre-amplification and custom primers targeting the V1-V3 region (515FB forward primer = GTGYCAGCMGCCGCGGTAA; 926R reverse primer= CCGYCAATTYMTTTRAGTTT) of the 16S rRNA gene. PCR products were verified visually by gel electrophoresis. Amplicon fragments were then sent to the Integrated Microbiome Resource, at Dalhousie University (https://imr.bio) and PCR-amplified using high-fidelity Phusion Plus® polymerase (New England Biolabs Inc.). Amplified DNA concentrations were then normalized, pooled, and sequenced via 6 runs on an Illumina MiSeq using 300 bp paired-end read chemistry. The sequencing runs yielded an average of at least 50,000 reads per sample.

tag: age at baseline (years)

tag: Sex

value: male

tag: ethnicity

value: asian

tag: smoking status

value: never smoker

tag: grade

value: moderate dysplasia

tag: lesion site

value: tongue


title: 1630

value: female

value: white


title: T-47D_RNAseq


title: BRC1915_CS20_P5_RNA-seq

description: Pseudoglandular organoids RNA-seq

value: Human fetal lung


title: 1552

value: mild dysplasia


title: SO_8069_KKK-D068_RNAseq


title: MMNK-1_RNAseq

source_name: immortalized cholangiocyte cell lines

value: immortalized cholangiocyte cell lines


title: 1496

value: floor of mouth


title: TFK-1_RNAseq

growth_protocol: We cultured KKU-055, KKU-156, KKU-213, KKU-214, KKK-D068, KKK-D131, KKK-D138 HuCCT-1 and HuH-28 in DMEM (Gibco) supplemented with 10%FBS and 1%penicillin streptomycin (Gibco). Four of CCA cell lines which are RBE, SSP-25, TFK-1, YSCCC were cultured in RPMI (Gibco) supplemented with 10%FBS and 1% penicillin streptomycin (Gibco). KKU-100 and HuCCA1 were grown in Ham-F12 (Gibco) supplemented with 10%FBS and 1% penicillin streptomycin (Gibco).  All cell lines were tested mycoplasma before perform an experiment.

extract_protocol:
RNA were extracted using Trizol, purified by Ambion RNA isolation kit (Invitrogen) and treat with PureLink DNase set (Invitrogen). RNA samples were quantified by measuring absorbance at 260nm with Qubit RNA HS assay kit. The integrity of RNA was analyzed by running on agarose gel electrophoresis and measuring RIN value by Agilent 2100 Bioanalyzer (Agilent Technologies). All CCA sample show high integrity of RNA with intact 28sRNA, intact 16sRNa and RNA integrity number(RIN)>8.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cholangiocarcinoma cell line TFK-1

tag: cell line source

value: Japanese


title: SSP-25_RNAseq

value: cholangiocarcinoma cell line SSP-25


title: BRC1915_CS20_P5_ATAC-seq

description: Pseudoglandular organoids ATAC-seq

value: Pseudoglandular organoids

value: Cystic


title: 1493

value: ever smoker

value: buccal or labial mucosa


title: 1431


title: 1466

value: male


title: 13393_CS23_P5_ATAC-seq

description: Pseudoglandular organoids ATAC-seq


title: 1386

value: hard palate or gingiva


title: MCF-7_RNAseq

value: breast cancer cell lines


title: 1380

value: asian

value: never smoker

value: tongue


title: KKU-214_RNAseq

value: cholangiocarcinoma cell line KKU-214

value: Thai


title: 1441

value: female

value: white

value: mild dysplasia


title: Small RNARevI-H2i2- white GLKD

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

country: France

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

data_processing: Adapters were trimmed and size selection was performed to retain only 18-29 nucleotide reads.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Total RNA extraction with TRIzol
Polyacrylamide gel size selection of 18-35 nucleotides, Library preparation using illumina TruSeq small RNA kit, Specific treatment anti 2S

value: ovaries

tag: genotype

value: RevI-H2i2- nos-Gal4- expressed dsRNA-white BDSC_3605

tag: time

value: 3-6 day old female


title: iR9-CHILP-27-2


title: iR9-CHILP-32-2


title: iR9-CHILP-34-2


title: iR9-CHILP-6-2


title: YSCCC_RNAseq

value: cholangiocarcinoma cell line YSCCC

value: Japanese


title: A549 cells, siRPS19, 72 hours (n=2)

city: Canberra

first: Ross

last: Hannan

state: ACT

address: John Curtin School of Medical Research

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

description:
RPS19 siRNA, biological replicate 2
7-siRPS19-1-72hr-n2-18-10-2013

data_processing:
The generated 50bp paired-end reads were aligned to the genome using TopHat v2.0.8b (Trapnell et al., 2009, PMID: 19289445) with default parameters and the reads counted using HTSeq (Anders et al., 2015, PMID: 25260700). Differential expression was calculated utilising the DESeq package (Anders and Huber, 2010, PMID: 20979621) in R (version 3.0.2). Absolute gene expression was defined by determining reads per kilobase per million (RPKM) as previously described (Mortazavi et al., 2008, PMID: 18516045).
ENSEMBL gene IDs were matched to Entrez Gene IDs, then RPKM data was intersected with high-throughput screening datasets (screening the siGENOME human SMARTpool siRNA library); either siOTP-NT (“p53 stabilisation” screen using the siOTP sequencing data) or siRPS19 siRNA (“modifiers of ribosomal stress” screen, using the siRPS19 sequencing data). We removed ‘non-expressed’ candidates from the screening datasets (based on an RPKM value cut-off of < 0.05); this finalised screening data (incorporating the RPKM data) is available on PubChem and within our bioRxiv manuscript (https://www.biorxiv.org/content/10.1101/2021.01.21.427535v1).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include HTseq outputs for individual replicates. For each condition (i.e. siOTP or siRPS19) a summary of counts across three replicates is provided as an Excel file. RPKM outputs for both the siOTP and siRPS19 analyses (averaged across 3 biological replicates) is also provided as a single Excel file.

source_name: Lung adenocarcinoma

growth_protocol: A549 cells (human lung adenocarcinoma, CCL-185, ATCC) were cultured in Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM:F12) with HEPES, supplemented with 10% foetal bovine serum containing 2mM L-Glutamine and incubated in humidified conditions at 37C with 5% CO2.

extract_protocol:
Total RNA was harvested using RNeasy mini kit (Qiagen) as per manufacturers' protocol.
Libraries for RNA-seq analysis were prepared using the Illumina TrueSeq RNAseq (standard, paired-end, 50bp) kit as per the manufacturers' protocol.

treatment_protocol: A549 cells were reverse transfected with 10 nM (final concentration) of RPS19 siGENOME SMARTpool siRNA (Horizon Discovery, M-003771-00) or non-targeting siRNA (ONTARGETplus (OTP) non-targeting control siRNA, Horizon Discovery, D-001810-10-50, prepared as per manufacturers’ instructions). Briefly, transfection mixes containing DMEM:F12 basal media with DharmaFECT1 (T-2001, final concentration of 1mL/mL) were prepared with siRNA and allowed to complex for 20 minutes. A549 cells (prepared in suspension in DMEM:F12 growth media) were then added on top and the cells incubated at 37oC in 5% CO2. At 24 hours’ post transfection, media was removed and replaced with fresh growth media, and transfected cells were incubated for a total of 72 hours prior to harvest of RNA samples.

value: Lung adenocarcinoma

value: RPS19 knockdown

value: Transfected with siRPS19 siRNA

value: 72 hours


title: KKU-156_RNAseq

value: cholangiocarcinoma cell line KKU-156


title: A549 cells, non-targeting siRNA (siOTP), 72 hours (n=3)

description:
Non-targeting siRNA, biological replicate 3
9-siOTP-1-72hr-n3-25-10-2013

value: Non-targeting (siOTP)

value: Transfected with non-targeting siRNA (siOTP)


title: iR9-CHILP-24-2


title: iR9-CHILP-8-2


title: iR9-CHILP-33-2


title: 1368

value: never smoker

value: moderate dysplasia

value: tongue


title: A549 cells, non-targeting siRNA (siOTP), 72 hours (n=2)

description:
Non-targeting siRNA, biological replicate 2
5-siOTP-1-72hr-n2-18-10-2013


title: KKU-213_RNAseq

value: cholangiocarcinoma cell line KKU-213

value: Thai


title: KKU-055_RNAseq

value: cholangiocarcinoma cell line KKU-055


title: iR9-CHILP-20-2


title: A549 cells, siRPS19, 72 hours (n=3)

description:
RPS19 siRNA, biological replicate 3
11-siRPS19-1-72hr-n3-25-10-2013


title: RBE_RNAseq

value: cholangiocarcinoma cell line RBE


title: 1347

value: male

value: white

value: ever smoker


title: 1343

value: female

value: mild dysplasia


title: iR9-CHILP-30-2


title: 1365

value: south asian


title: iR9-CHILP-25-2


title: KKU-100_RNAseq

value: cholangiocarcinoma cell line KKU-100


title: 1351


title: iR9-CHILP-19-2


title: A549 cells, siRPS19, 72 hours (n=1)

description:
RPS19 siRNA, biological replicate 1
3-siRPS19-1-72hr-n1-11-10-2013

value: Lung adenocarcinoma

value: RPS19 knockdown

value: Transfected with siRPS19 siRNA

value: 72 hours


title: 1244

value: never smoker

value: hard palate or gingiva


title: HuCCA-1_RNAseq

value: cholangiocarcinoma cell line HuCCA-1


title: 1167

value: tongue


title: iR9-CHILP-12-2


title: HuCCT-1_RNAseq

value: cholangiocarcinoma cell line HuCCT-1

value: Japanese


title: iR9-CHILP-2-2


title: KKK-D138_RNAseq

value: cholangiocarcinoma cell line KKK-D138

value: Thai


title: 1314

value: male

value: white

value: ever smoker

value: moderate dysplasia


title: iR9-CHILP-15-2


title: Capi2173

first: Shuyu

last: Liu

address: Tennis Court

department: The Gurdon Institute

data_processing:
Illumina software used for conventional basecalling.
Reads were aligned to GRCh38 genome assembly (hg38) in hisat2 (2.0.5).
Reads were summarised using featureCounts (1.5.0-p3).
Differentially gene expression analysis was performed using DESeq2 (1.20.0).
Assembly: Ensembl Homo_sapiens.GRCh38 (hg38)
Supplementary files format and content: A text file (csv format) includes FPKM values for each sample

growth_protocol: Fetal lung tip organoids were cultured in Matrigel in self-renweing (SN) culture medium.

extract_protocol:
Total RNA was harvested from lung organoids using RNeasy Kit (Quiagen, 74004) and quality control was performed on Agilent 2200 Tapestation with High Sensitivity RNA Screen Tape (Agilent, 5067-5579).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNS synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: 200 nM MEKi (PD0325901), 200 nM ERKi (SCH772984) or 200 nM AKTi (Capivasertib) were added to the SN culture for 4 days and RNA samples were isolated.

tag: sample id

tag: developmetal age

value: 11 pcw

value: AKT inhibitor treated


title: KKK-D131_RNAseq

value: cholangiocarcinoma cell line KKK-D131


title: ERKi1915

value: 7 pcw

tag: passage number

value: ERK inhibitor treated


title: Capi1915


title: ERKi2173


title: ERKi14580

value: 9 pcw


title: HuH-28_RNAseq

value: cholangiocarcinoma cell line HuH-28


title: 1163

value: never smoker


title: Capi14580


title: iR9-CHILP-10-2

tag: cell type


title: A549 cells, non-targeting siRNA (siOTP), 72 hours (n=1)

description:
Non-targeting siRNA, biological replicate 1
1-siOTP-1-72hr-n1-11-10-2013

tag: cell line

tag: tissue

value: Lung adenocarcinoma

value: Non-targeting (siOTP)

value: Transfected with non-targeting siRNA (siOTP)

value: 72 hours


title: 1133

value: female

value: mild dysplasia

value: tongue


title: MEKi2173

value: MEK inhibitor treated


title: 1072

value: male

value: white

value: hard palate or gingiva


title: KKK-D068_RNAseq

value: cholangiocarcinoma cell line KKK-D068

value: Thai

tag: rrid


title: iR9-CHILP-14-1

tag: strain


title: SN2173

value: 11 pcw

tag: treatment

value: SN control


title: MEKi1915

value: 7 pcw


title: 1035

tag: age at baseline (years)

tag: Sex

value: never smoker


title: GCMT-treated IMR-90 nuclei

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Reads were mapped with BMap
Alignments were summerized with MPTC
Methylation levels and read coverage were exported with MetExport
Assembly: hg19
Supplementary files format and content: bedGraph

source_name: IMR-90 nuclei treated with GCMT

growth_protocol: The IMR-90 cells were grown in MEM media supplemented with 10% FBS and antibiotics at 30°C

extract_protocol:
The genomic DNA was extracted from the GCMT-treated fixed yeast cells.
After bisulfite treatment with EZ methylation gold kit, and served for tPBAT protocol

treatment_protocol: The cells were lysed with a solution containing 0.1% NP40 to obtain nuclei. The nuclei was treated with GCMT (M.CviPI).

value: GCMT (M.CviPI)


title: WT-CHILP-9-1

value: WT-CHILP


title: iR9-CHILP-17-1


title: SN1915


title: iR9-CHILP-12-1


title: WT-CHILP-8-1


title: WT-CHILP-7-1


title: TgPru infected HFF_rep4

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum BLVD IDRB 403

department: Internal Mediciine

country: USA

institute: University of South Florida

description:
PruΔku80Δhxgprt
J682_AH7MVWBCXY_Lane1_TAGGCATG-TATCCTCT_Pru-Infected_HFF-downsample.sorted.bedGraph

data_processing:
The ATAC-seq processing followed the “pyflow-ATACseq” workflow (https://zenodo.org/record/1043588#.XKoxbqR7lEY).
Raw sequenced reads were aligned to a combined Homo sapiens (hg38)-T. gondii (ME49 v9.0) genome.
Reads mapping to the mitochrondria were removed and broad peaks were called using MACS2 (v2.1.0).
Finally, we used the MACS2 output as input for nucleoATAC to identify nucleosome footprinting.
Replicates were merged together using bedtools merge (v2.24.0) to get a consensus set of peaks for uninfected, RH-infected,and Pru-infected cells.
Assembly: Combined Homo sapiens (hg38)-Toxoplasma gondii (ME49 v9.0) genome.
Supplementary files format and content: BedGraph files were generated using bedtools (v2.28.0) for visulization.

source_name: Human foreskin fibroblasts and Toxoplasma

growth_protocol: Human foreskin fibroblasts (HFFs) were grown in DMEM supplemented with 10% FBS; 2 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
50,000 cells were resuspended in 50 µl of cold lysis buffer and centrifuged at 4°C for 10 min at 1000×g. The nuclei pellet was immediately resuspended in the transposition reaction mix and incubated for 30 min at 37°C. All transposed samples were purified using the Qiagen MiniElute Kit in 12 μl of buffer EB (10mM Tris-HCl, pH 8.0).
Following purification, ATAC-seq libraries were amplified by PCR with NEBNext High-Fidelity 2x PCR Master Mix and 1.0 μM of Nextera Barcoded PCR primers (PCR conditions: one cycle of 72°C for 5min and 98°C for 30 sec; 10 cycles of 98°C for 10 sec, 63°C for 30 sec and 72°C for 1 min). All amplified libraries were purified using the Qiagen MiniElute Kit in 22 μl of buffer EB.

treatment_protocol: Confluent HFFs in T25 tissue culture flasks were infected with either Toxoplasma gondii RHΔku80Δhxgprt (Type I) or PruΔku80Δhxgprt (Type II) at a multiplicity of infection of one tachyzoite per cell. At 24 hours post infection, four T25 tissue culture flasks each of uninfected, RH-infected and Pru-infected HFFs were washed with PBS and the cell monolayers were scraped into cold PBS and then collected by centrifugation at 4°C for 10 min at 700×g.

value: Pooled primary HFFs from multiple donors

tag: agent

value: Toxoplasma RHdeltaku80deltahxgprt

value: Pru-infected


title: WT-CHILP-6-1


title: TgPru infected HFF_rep3

description:
PruΔku80Δhxgprt
J687_AH7MVWBCXY_Lane2_GGACTCCT-TATCCTCT_Pru-Infected_HFF-downsample.sorted.bedGraph


title: RE1KO,BRBseq,multiplexed

city: Bar Harbor

first: Kousuke

last: Mouri

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Reads were mapped using STAR (v2.7.6a, --outFilterMultimapNmax 1)
Reads were demultiplexed by BRBseqTools (v1.3.1)
Mapped reads were counted by BRBseqTools (v1.3.1).
Assembly: GRCh38
Library strategy: BRB-seq

growth_protocol: 37C with 5% CO2 supplementation

extract_protocol:
Total RNA was purified by using Rneasy mini (QIAGEN) from homogenized cells.
500 ng of total RNA for each replicate was reverse-transcribed, pooled, and purified in two columns of Monarch PCR & DNA Clean up kit, followed by second-strand synthesis and tagmentation

treatment_protocol: Cells were electroporated by using NEON transfection system, recovered in culture medium for 24 hours, and selected by Puromycin for 48 hr followed by a recovery for 8-9 days.

value: Colon cancer cell


title: WT-CHILP-5-1


title: CCMT-treated IMR-90 nuclei

data_processing:
Reads were mapped with BMap
Alignments were summerized with MPTC
Methylation levels and read coverage were exported with MetExport
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: IMR-90 nuclei treated with CCMT

extract_protocol:
The genomic DNA was extracted from the CCMT-treated fixed yeast cells.
After bisulfite treatment with EZ methylation gold kit, and served for tPBAT protocol

treatment_protocol: The cells were lysed with a solution containing 0.1% NP40 to obtain nuclei. The nuclei was treated with CCMT (M.CviQIX).

value: CCMT (M.CviQIX)


title: MEKi14580

value: 9 pcw

value: MEK inhibitor treated


title: Untreated IMR-90 nuclei

source_name: IMR-90 nuclei without MTase treatment


title: TgPru infected HFF_rep2


title: TgPru infected HFF_rep1


title: WT-CHILP-4-1


title: WT-CHILP-31-1


title: arf2-6 T5 Rep2

type: RNA

city: York

first: Katherine

last: Denby

address: Department of Biology

institute: University of York

description: arf2-6 plants 5 days after dark treatment Rep 2

hyb_protocol: Hybridisation was carried out according to manufacturer's instructions (Roche, Nimblegen)

scan_protocol: Slides were scanned using a Nimblegen array scanner at 532nm (Cy3)

data_processing:
Processing of array data was performed using ANAIS (http://anais.versailles.inra.fr/) applying RMA background correction and quantile normalization.
Analysis of expression differences between Col-0 and arf2-6 at each time point was performed using ANAIS (http://anais.versailles.inra.fr/). The Benjamini and Hochberg false discovery rate (FDR) multiple testing correction (Benjamini and Hochberg 1995) was applied and a cutoff of adjusted P < 0.05 was used to identify differentially expressed genes.

organism: Arabidopsis thaliana

label_protocol: Labelling was carried out according to manufacturer's instructions (Roche, Nimblegen)

growth_protocol: Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1). Arabidopsis plants were grown under a 16:8 h light:dark cycle at 23°C, 70% humidity, and light intensity of 120 μM photons m-2s-1 for three weeks

extract_protocol: Extracted using Trizol (Invitrogen) and  cleaned up with RNeasy mini plant kit (Qiagen)

treatment_protocol: 3‐week old rosettes were cut and transferred to water‐saturated filter paper in sterile petri dishes and stored at 20°C in complete darkness. Leaf 5 from three rosettes per genotype was harvested at three and five days of dark treatment.

value: 5 days dark treatment

value: leaf

tag: replicate


title: arf2-6 T3 Rep3

description: arf2-6 plants 3 days after dark treatment Rep 3

value: 3 days dark treatment


title: SN14580


title: arf2-6 T5 Rep3

description: arf2-6 plants 5 days after dark treatment Rep 3


title: arf2-6 T3 Rep2

description: arf2-6 plants 3 days after dark treatment Rep 2


title: arf2-6 T5 Rep1

description: arf2-6 plants 5 days after dark treatment Rep 1


title: arf2-6 T3 Rep1

description: arf2-6 plants 3 days after dark treatment Rep 1


title: GR-Rep2

city: Beijing

first: Ting

last: Peng

address: Beijing haidiang

institute: PKU

data_processing:
library strategy: CUT&Tag
Fastq files were trimmed using TrimGalore and aligned to the human genome assembly (hg19) with Bowtie2.
Then peaks were called by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: Natural Killer Cell line

growth_protocol: NK92 cells were cultured under standard conditions (37℃，5% CO2，humidified atmosphere) in alpha-mem medium contains 20% fetal bovine serum (Gibco) combined with 100U IL-2 and 1% penicillin-streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA was isolated with antibody. Antibody was purchased from abcam. The catalog number is GR (ab3671), H3K27 (ab4729).
A kit (Vazyme TD901 kit) was used to generate DNA libraries

value: Natural Killer Cell line

tag: antibody


title: WT-CHILP-29-1


title: GR-Rep1


title: H3K27ac-Rep2


title: H3K27ac-Rep1


title: WT-CHILP-28-1


title: WT-CHILP-3-1


title: COL0 T5 Rep3

description: Col-0 plants 5 days after dark treatment Rep 3

value: wild type


title: TgRH infected HFF_rep1

description:
RHΔku80Δhxgprt
J682_AH7MVWBCXY_Lane1_AGGCAGAA-CTCTCTAT_RH-Infected_HFF-downsample.sorted.bedGraph

value: RH-infected


title: COL0 T5 Rep2

description: Col-0 plants 5 days after dark treatment Rep 2


title: TgRH infected HFF_rep3


title: Uninfected HFF_rep3

description: J682_AH7MVWBCXY_Lane1_CGTACTAG-AGAGTAGA_Uninfected_HFF-downsample.sorted.bedGraph

source_name: Human foreskin fibroblasts

value: uninfected


title: COL0 T5 Rep1

description: Col-0 plants 5 days after dark treatment Rep 1


title: COL0 T3 Rep3

description: Col-0 plants 3 days after dark treatment Rep 3


title: TgRH infected HFF_rep4

description:
RHΔku80Δhxgprt
J682_AH7MVWBCXY_Lane1_TCCTGAGC-CTCTCTAT_RH-Infected_HFF-downsample.sorted.bedGraph


title: Uninfected HFF_rep4

description: J682_AH7MVWBCXY_Lane1_TAAGGCGA-AGAGTAGA_Uninfected_HFF-downsample.sorted.bedGraph


title: WT-CHILP-25-1


title: Uninfected HFF_rep2


title: Control strain rep2

city: Seville

first: Peter

last: Askjaer

address: Universidad Pablo de Olavide, Carretera de Utrera, km 1

country: Spain

institute: Andalusian Centre for Developmental Biology

data_processing:
Sequencing fastq files were filtered to discard reads that do not start with the DamID adapter followed by GATC (“CGCGGCCGAGGATC”) using R Studio and the damid.seq.R pipeline version 0.1.3 (available at github.com/damidseq/RDamIDSeq). Retained fragments were mapped to C. elegans UCSC genome version ce11 with the same pipeline, which produced 9.5-41.9 million uniquely mapped reads per sample.
Normalization of Dam::RPB-6 reads to GFP::Dam reads was performed using the damidseq_pipeline package (https://owenjm.github.io/damidseq_pipeline/) on the bam files generated by the damid.seq.R script.
Gene occupancy was computed as log2(Dam::RPB-6/GFP::Dam) with polii.gene.call  (https://github.com/owenjm/polii.gene.call) using bedgraph output files from the damidseq_pipeline and WBCel235 gene annotation.
A false discovery rate (FDR) of 0.05 was used as threshold to call transcribed genes.
Assembly: ce11
Supplementary files format and content: bedgraph files from damidseq_pipeline script; 1 file per replica and 1 file with combined data; contain log2 scores for each GATC fragment.
Supplementary files format and content: csv file polii.gene.call from script; contains for each gene log2 score, number of GATC fragments and FDR.
Library strategy: DamID

organism: Caenorhabditis elegans

source_name: C. elegans L4 larvae

growth_protocol: Worms were grown at 20°C for at least two generation on NGM plates seeded with E. coli GM119 dam- bacteria. Eggs were obtained by sodium hypochlorite treatment  and incubated in M9 containing 0.01% Tween-20 (M9-T) overnight at 18°C without food. For each strain and replica, four 100 mm NGM plates with a lawn of GM119 were seeded each with approximately 1000 synchronized L1 larvae and incubated at 20°C for 48 h until reaching L4 stage.

extract_protocol:
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1 min in liquid nitrogen; 3 min in 37°C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504). Two hundred ng of genomic DNA was used as input in the DamID protocol that included an improved pool of AdR primers as described (doi: 10.1007/978-1-0716-2337-4_11). Dam-methylated fragments were amplified with 14 PCR cycles and quality checked on an Agilent Bioanalyzer 2100.
Libraries were prepared using 50 ng of PCR-amplified fragments and NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). Library amplicons size range distribution was checked as before, pooled and re-purified with 1x volume SpeedBeads (doi: 10.1007/978-1-0716-2337-4_11) followed by sequencing at EMBL GeneCore using a NextSeq 500 (Illumina).

treatment_protocol: Larvae were washed off the plates with M9-T, collected in 15 ml tubes and washed 8 times in M9-T. Next, worms were transferred to 1.5 ml tubes washed twice in M9-T. The supernatant was aspired to leave ~30 µl and tubes were snap frozen in liquid nitrogen and stored at -80°C until used.

tag: flp recombinase

value: Hypodermis (dpy-7p::FLP)

tag: condition

value: GFP::Dam in hypodermis


title: Control strain rep1


title: Hypodermal RAPID rep2

value: Dam::RPB-6 in hypodermis


title: WT-CHILP-22-1

value: WT-CHILP


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M6 (biol rep 6)]

city: New Brunswick

first: Mijung

last: Kwon

state: NJ

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

description: Matrix M6

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed to remove adapter sequences using Trimmomatic v.0.36 (RRID:SCR_011848), and the trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2., and were used for downstream differential expression analysis.
Using DESeq2, the gene hit counts within each sample were normalized.
Assembly: mm10
Supplementary files format and content: CSV file includes NORMALIZED gene hit counts for all 12 samples as a matrix.

source_name: Subcutaneous tumors

growth_protocol: mTc11 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

treatment_protocol: 1 X 10^6 cells of mTc11 clones were suspended in growth factor-reduced Matrigel (Corning #356231; 1:1 ratio (v:v)) and subcutaneously injected in 8 week-old male C57BL6/J mice. Tumors were harvested at 24 days after injection and snap-frozen. Frozen tumors were processed to obtain total RNA.

value: Subcutaneous tumors

value: Mouse lung cancer cells

tag: genotype

value: Filip1l KD


title: Input control-4 DLD-1/RAD21L+STAG3+SMC1B

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

description: control

data_processing:
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
reads trimmed of adapters and  low quality reads using fastp (doi.org/10.1093/bioinformatics/bty560)
clean FASTQ files  generated.
paired end reads (R1 and R2 FASTQ files) were treated as single reads. R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Genome_build: hg38 (GRCh38.p12, NCBI Assembly ID: 5800238)
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

source_name: colon epithelium

growth_protocol: K562, hTERT RPE-1, or DLD-1 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. Cells infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, 300 µg/ml zeocin, 1 µg/ml puromycin, or 200 µg/ml hygromycin B, dependent on the vector's marker, followed by the selection of individual clones.

extract_protocol:
Cells were fixed at 1% formaldehyde for 10 min at room temperature and quenched with 0.125 mM glycine for 5 min. For some experiments a dual crosslinking was used, by incubating the cells in 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) (Sigma) in PBS for 45 min at RT under gentle shaking. Then, 1% formaldehyde was added and the incubation left to proceed for 20 min, after which the fixation was quenched with 0.125 mM glycine for 5 min at RT. Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), and the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina system with Illumina-provided protocols for paired-end sequencing

treatment_protocol: For ChIP-seq experiments, stable Tet-On transgenic cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours

value: epithelial tumor cells DLD-1

value: colorectal adenocarcinoma

tag: chip antibody


title: DMSO-2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: MOLM13 cell lines (DMSO treated)

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human GRCh37 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene list, sample metadata, rawcount matrix

source_name: MOLM13 cell lines (DMSO treated)

growth_protocol: MOLM-13 were grown in RPMI medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
After 24hs of incubation the cells were collected and RNA was extracted using Qiagen RNeasy kit for RNA sequencing
The RNA sequencing was done at Cincinnati Children’s Hospital Medical Center. The conditions for sequencing were: Poly A, 75 bp pair end single stranded with 20 million reads

treatment_protocol: The cells were treated with 2uM UC-764864 or DMSO

value: DMSO


title: Uninfected HFF_rep1

value: Pooled primary HFFs from multiple donors


title: WT-CHILP-24-1

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2 (Vazyme, N711).
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme, TD503).


title: TgRH infected HFF_rep2

value: Toxoplasma RHdeltaku80deltahxgprt


title: WT-CHILP-21-1


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M5 (biol rep 5)]

description: Matrix M5


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M4 (biol rep 4)]

description: Matrix M4


title: DMSO-3

description: MOLM13 cell lines (DMSO treated)


title: WT-CHILP-26-1


title: WT-CHILP-27-1


title: DMSO-1

description: MOLM13 cell lines (DMSO treated)


title: Hypodermal RAPID rep1


title: WT-CHILP-23-1


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M3 (biol rep 3)]

description: Matrix M3


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M2 (biol rep 2)]

description: Matrix M2


title: WT-CHILP-18-1


title: UC64-3

description: MOLM13 cell lines (UC64 treated)

source_name: MOLM13 cell lines (UC64 treated)


title: WT-CHILP-17-1

source_name: common helper innate lymphoid progenitors


title: WT-CHILP-2-1


title: UC64-1

description: MOLM13 cell lines (UC64 treated)


title: COL0 T3 Rep1

description: Col-0 plants 3 days after dark treatment Rep 1

value: 3 days dark treatment

value: leaf


title: UC64-2

description: MOLM13 cell lines (UC64 treated)


title: Subcutaneous tumors from mTc11 cells, shControl [L6 (biol rep 6)]

description: Matrix L6

value: WT


title: WT-CHILP-19-1


title: Subcutaneous tumors from mTc11 cells, Filip1l KD [M1 (biol rep 1)]

description: Matrix M1


title: Subcutaneous tumors from mTc11 cells, shControl [L5 (biol rep 5)]

description: Matrix L5


title: WT-CHILP-15-1


title: Input control-3 DLD-1/REC8+STAG3+SMC1B

description: control


title: ShSCRAMBLE-3

description: MOLM13 shRNA treated

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human GRCh37 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene list, sample metadata, rawcount matrix

source_name: MOLM13 shRNA treated

extract_protocol: RNA was extracted using Qiagen RNeasy kit following manufacturer instructions for RNA sequencing.  The RNA sequencing was done at Cincinnati Children’s Hospital Medical Center. The conditions for sequencing were: Poly A, 75 bp pair end single stranded with 20 million reads.

treatment_protocol: MOLM-13 cells were transduced with the short-hairpin-containing lentivirus and incubated for up to 15 days. After culture with fresh medium, transduced cells were sorted for GFP-positive cells using a MoFlo XDP sorter (Beckman Coulter) and used for experiments.

tag: shRNA

value: shSCRAMBLE


title: WT-CHILP-13-1

data_processing:
Bcl2fastq (version 2.16.0.10) convert .bcl files into fastq files.
Fastq files were aligned to mm10 genome. *.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Assembly: mm10
Supplementary files format and content: CHILP_TPM_Matrix.txt: Matrix table with TPM value for every gene and every cell.


title: COL0 T3 Rep2

description: Col-0 plants 3 days after dark treatment Rep 2

value: wild type


title: ShSCRAMBLE-2

description: MOLM13 shRNA treated


title: shSCRAMBLE-1

description: MOLM13 shRNA treated


title: WT-CHILP-16-1


title: Input control-3 DLD-1/RAD21L+STAG3+SMC1B

description: control


title: Input control-1 DLD-1/RAD21L+STAG3+SMC1B

description: control


title: ShUBE2N3-3

description: MOLM13 UBE2N knockout

source_name: MOLM13 UBE2N knockdown


title: shUBE2N3-2

description: MOLM13 UBE2N knockout


title: ShUBE2N3-1

description: MOLM13 UBE2N knockout


title: WT-CHILP-1-1


title: Input control-2 DLD-1/REC8+STAG3+SMC1B

description: control


title: Subcutaneous tumors from mTc11 cells, shControl [L2 (biol rep 2)]

description: Matrix L2


title: Subcutaneous tumors from mTc11 cells, shControl [L4 (biol rep 4)]

description: Matrix L4


title: Input control-4 DLD-1/REC8+STAG3+SMC1B

description: control


title: 4A_S18_R1_001 (paired)

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
CLC Genomics Workbench v 21.0.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Reads were aligned to the rRNA track of CP063198_sRNA and unmapped reads used for RNA-seq
Trimmed sequence reads were mapped first to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Unmapped sequence reads were then mapped to CP063198_sRNA using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CP063198_sRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).RNA was extracted from 2-3 mice before pooling RNA to form triplicate samples. For bacteria, we utilized three input controls as replicates and again pooled from 2-3 mice for all bacterial samples.
Samples were rRNA depleted using RiboZero Plus (Illumina) and libraries for the 12 mouse samples and 3 input bacteria cDNA samples were sequenced using the Illumina Stranded RNA sequencing platform.

value: Skin

value: Diabetic uninfected


title: ZKD_MUT1_IP

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
Reads were psuedoaligned using Kallisto (v0.44.0) to human gene transcript annotations (hg38) to determine transcript abundance.
Kallisto output was imported into R for use with DESeq2 (v1.24.0) to determine log2 fold change using a likelihood ratio test where crosslinked RNA fractions were normalized to inputs for each LIN28B protein expressed. We used a gene count cutoff of 5.
genome build: hg38
processed data files format and content: Text file containing DESeq2 output of RIP sequencing analysis. Comparison is WT, CSD or ZKD LIN28B RIP fractions normalized to RNA input and subsequently compared between full RNA binding deficient LIN28B mutant denoted MUT (e.g. log2FC(LIN28BWT/MUT). Data was filtered for protein coding genes as well as genes detected across multiple datasets reported in this manuscript. Additional processed files are normalized counts for each set of comparisons (e.g. CSD_MUT vs MUT).

source_name: LIN28B-KO BE2C cells

growth_protocol: BE2C (ATCC #CRL-2268) were maintained in 1:1 DMEM/F12:MEM media with 10% inactivated fetal calf serum, 1ug/ml penicillin, and 1U/ml streptomycin. Cell lines were purchased for the purposes of this study, are not among commonly misidentified cell lines (per ICLAC), and tested negative for mycoplasma contamination

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen # 15596018) and RNeasy Plus Mini Kit (Qiagen # 74136). RNA concentration was assessed with Quant-iT™ Qubit RNA BR Assaykit (Invitrogen # Q10210)
PolyA selection with NEBNext® Poly(A) mRNA Magnetic Isolation Module. Paired-end libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to manufacturer's protocol

treatment_protocol: No specific treatment applied

tag: fraction

value: immunoprecipitated

tag: lin28b expression

value: ZKD mutant

tag: tag

value: FLAG


title: Subcutaneous tumors from mTc11 cells, shControl [L1 (biol rep 1)]

description: Matrix L1

tag: tissue

value: Subcutaneous tumors

tag: cell line

tag: cell type

value: Mouse lung cancer cells


title: WT-CHILP-11-1

tag: strain

value: WT-CHILP


title: 2C_S14_R1_001 (paired)

tag: treatment

value: Non-diabetic uninfected


title: WT-ILC-9-1

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Assembly: mm10
Supplementary files format and content: Matrix table with TPM value for every gene and every cell

source_name: Innate lymphoid cells

growth_protocol: The single regenerative R9-ILCs were sorted from the intestine of Rag2-/-Il2rg-/- recipient mice 3 weeks after transplantation and the WT-ILCs were sorted from the intestine of wild type mouse (C57BL/6, CD45.2 strain, 8-week-old) by folw cytometry.

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2 (Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single ILCs were sorted for RNAseq analysis.

tag: time

value: 8 weeks old

value: intestine of wildtype mouse

value: Innate lymphoid cells


title: ZKD_MUT3_IP


title: CSD_MUT2_IP

value: CSD mutant


title: WT-CHILP-10-1


title: Input control-2 DLD-1/RAD21L+STAG3+SMC1B

description: control

value: epithelial tumor cells DLD-1

value: colorectal adenocarcinoma


title: WT-CHILP-12-1


title: WT-CHILP-14-1


title: MUT3_IP

value: mutant


title: Subcutaneous tumors from mTc11 cells, shControl [L3 (biol rep 3)]

description: Matrix L3

value: WT


title: 4C_S20_R1_001 (paired)

value: Skin


title: Input control-2 DLD-1

description: control


title: 2B_S13_R1_001 (paired)


title: ZKD_MUT2_IP


title: WT-ILC-32-1


title: RDseq, ent1, rep2

city: Wien

first: Bernardo

middle: P

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
Paired-end sequencing reads were demultiplexed using specific barcodes and mapped to the dedicated bowtie index using Bowtie v.1.2.2 (-X 150 ‐v 3 -m 1 –quet –best –strata). The UMI sequence was incorporated to the read ID on the demultiplexing step. Mapped read pairs, fragments, were collapsed by coordinates (oligoID, start, end, strand) and by UMI, i.e., by removing duplicate fragments with identical coordinates if their UMIs differed by <= 2 out of the 10 nucleotides. To calculate position-specific coverage for each frame, oligonucleotide-centric coordinates were transformed into TFs-centric coordinates and total coverage was calculated using the coverage function from R package GenomicRanges [v.1.32.7]. Fragment coverage was visualized using the linear genome at the UCSC Genome Browser.
We calculated enrichments, hypergeometric P-values, and Benjamini–Hochberg (BH)‐corrected false discovery rates [FDRs] between the coverage values in GFP- and GFP+ cells. To define repressive domain (RD) regions, we only considered regions with a minimal coverage of at least 10 fragments in GFP+ cells, and selected regions with a minimal enrichment ≥ 1.5‐fold and a hypergeometric P‐value ≤ 1 × 10−5 across a minimal length of ≥ 60 bp (20 amino acids), which we extended to include flanking coding sequences (CDS) until P > 1 × 10−3 over ≥ 60 bp (20 amino acids).
Assembly: Custom oligo library
Supplementary files format and content: coveragePerOligo: coverage files for each oligo with respective enrichments between GFP-neg and GFP-pos cells, and DNA and AA sequence
Supplementary files format and content: RD_calls: Repressive domain regions identified in each screen

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Medium (Gibco; cat. no. 21720-024) supplemented with 10% heat inactivated FBS (Sigma; cat. no. F7524)

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Prep Kit.
mRNAs were enriched with Dynabeads Oligo-dT25 (Invitrogen), followed by a DNA digest with Turbo DNase (Ambion).
mRNAs were cleaned up with AMPure XP DNA beads (Agencourt; ratio sample/beads 1:1.8) and then reverse transcribed with Superscript III (50°C for 60 min, 70°C for 15 min; Invitrogen 18080085) and a primer binding within the poly-A site of candidate mRNAs (reverse_transcription_rv: CTCATCAATGTATCTTATCATGTCTG).
Next, RNA was digested with Rnase A (Thermo) for 1 h at 37°C, followed by bead cleanup of the remaining DNA (ratio sample/beads 1:1.4).
All subsequent PCR reactions were prepared using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2602). A second strand PCR was performed with a primer binding upstream of the intron sequence which is part of candidate mRNA (2nd_strand_primer_fw: TTGGTAAAGCCACCATGGAAAAG*G) (98°C for 60 s, 65°C for 30 s, 72°C for 90 s), followed by bead cleanup (ratio sample/beads 1:1.4).
In the next step, unique molecular identifiers (UMIs) were introduced to the 3’ ends of DNA fragments in a linear PCR with a primer binding to the Illumina i7 adaptor sequence (UMI_primer_rv: CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G) (98°C for 60 s, 65°C for 30 s, 72°C for 90 s).
After bead cleanup (ratio sample/beads 1:1.4), the generated fragments were PCR-amplified (98°C 45 s, followed by 16 cycles, 98°C 15 s, 65°C 30 s, 72°C 70s) using two candidate-specific primers (junction_PCR_fw: AAGCCACCATGGAAAAG*G*C*C*A*T and junction_PCR_rv: CAAGCAGAAGACGGCATACG*A), one of which spans the splice junction of the mhc16 intron (5 and 1 nucleotides at the 3’ ends are protected by phosphorothioate bonds, respectively).
After another bead cleanup (ratio sample/beads 1:1), candidate fragments were amplified (98°C 45 s, followed by 6-15 cycles, 98°C 15 s, 65°C 30 s, 72°C 70s) with the following primers: i5: aatgatacggcgaccaccgagatctacacXXXXXXXXacactctttccctacacgacgctcttccgatct (XXXXXXXX indicates the position of the index sequence for NGS) and the reverse primer seq_ready_rv: CAAGCAGAAGACGGCATACGAGA*T. PCR products were purified by Agencourt AMPure XP DNA beads (ratio sample/beads 1:0.9), pooled, and subjected to NGS.

treatment_protocol:
Drosophila S2 GFP reporter cell lines were transfected with a Gal4-DBD-candidate library containing 209,495 150 bp candidate fragments tiling the coding sequences of 1133 transcription-related genes from Drosophila melanogaster
Three days after transfection, cells were sorted into GFP-positive and GFP-negative fractions on a BD FACSAria III cell sorter.

value: Schneider S2

value: cells transfected with Gal4-DBD-candidate library tiling transcription-related Drosophila melanogaster genes


title: RDseq, zfh1, rep1


title: WT-ILC-31-2

first: yunqing

last: Lin


title: WT-ILC-31-1


title: RDseq, zfh1, rep2


title: WT-ILC-9-2


title: WT-ILC-7-2


title: WT-ILC-6-2


title: WT-ILC-32-2


title: W34/70 9.7 minimal medium rep 3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
For each strain a reference genome was created by combining chromosomes from S. cerevisiae and S. eubayanus and adjusting for SNVs detected through WGS of the lab strains (88k and 126k for CBS1538 and W 34/70, respectively)
Paired-end reads were mapped through STAR with parameters --outMultimapperOrder Random and --outSAMmultNmax 1
STAR results were filtered for high-quality mappings using samtools view with the parameter -q 255
Reads were aggregated using featureCounts with the parameters -B and -P
Differentially expression analysis was carried out with DESeq2 through iDEP9.1 (http://bioinformatics.sdstate.edu/idep/)
Assembly: Saccharomyces cerevisiae S288C R64-2-1_20150113 and Saccharomyces eubayanus strain FM1318 (04-NOV-2015) with SNV modifications based on whole-genome sequencing of CBS1538 and W 34/70
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces pastorianus

source_name: Lager yeast

growth_protocol: For the samples labelled "Minimal Medium", cells were grown in 2% YPDM overnight, washed with sterile water and inoculated at a cell density of 1x10^6 cells/mL into 60 mL of minimal medium (0.17% Yeast Nitrogen Base w/o amino acids and ammonium salts supplemented with 1% of dextrose and 1% of maltose, and 0.5% (NH4)2SO4 as a nitrogen source. The cultures were grown at 20ºC, in triplicate, and cells were harvested in the exponential phase. For fermentation samples (Day 2 and Day4) , cells were propagated in 200 mL of 4% YPDM at 25ºC for two days and were pitched into wort at a cell density of 1.5x10^7/mL. Fermentations (10mL)  were carried out in 10% wort containing 1mM ZnSO4 in triplicate at 13ºC without shaking. 10mL aliquots of the starting fermentation culture were added to 15mL glass tubes, each fitted with a water trap airlock attached to a bung.

extract_protocol:
Cells were resuspended in 400 µL of buffer containing 50 mM of NaOAc, pH 5.2, 10 mM EDTA pH 8.0 and 40 mL of 10% SDS, 400 µL of Phenol-Chloroform-Isoamyl alcohol (PCA; 25:24:10), pH 4.2, and 100 mL of acid washed glass beads were added. The tubes were placed in a heat block at 65ºC for 10 min and vortexed intermittently. The samples were placed on ice for 5 min. After centrifugation, the supernatant was re-extracted with PCA, pH 4.2 and then once with chloroform. Nucleic acids in the supernatant were precipitated, washed twice with 70% ethanol and then resuspended in 100 µL RNase-free H2O. The RNA concentration was measured using a Nanodrop spectrophotometer and RNA integrity was checked by Agilent 2100  Bioanalyzer as per manufacturer’s instructions.
Paired-end (150bp)  Illlumina

treatment_protocol: Cells at a concentration of 1x107 cells·mL-1 were inoculated in SC medium containing a final concentration of radicicol of 20, 40 and 100 µg · mL-1 for 24 and 48h. After the treatment, aliquots of 100 µL were plated onto minimal medium agar plates containing 75 µg·mL-1 of B2TA or 200 µg· mL-1 of PFPA. To ensure that mutants retained the phenotype of resistance to amino acid analogues, the colonies were re-streaked onto agar plates of minimum media containing the amino acid analogues at least three times. Resistant colonies were designated by a code based on the mutagenesis treatment and conditions

value: W34/70 mutant strain

value: minimal medium


title: Input control-1 DLD-1/REC8+STAG3+SMC1B

description: control


title: CSD_MUT1_IP

value: immunoprecipitated

value: FLAG


title: CSD_MUT3_IP


title: WT-ILC-29-2

city: Guangzhou, China

address: Building 3, No.188 Kaiyuan Avenue, Huangpu District, Guangzhou

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)


title: 2A_S12_R1_001 (paired)


title: 4B_S19_R1_001 (paired)

value: Diabetic uninfected


title: Input control-1 DLD-1

description: control


title: WT-ILC-5-2


title: ZKD_MUT2_input

value: input

value: ZKD mutant


title: W34/70 9.7 minimal medium rep 1


title: WT-ILC-29-1

value: 8 weeks old

value: intestine of wildtype mouse


title: WT1_IP

value: wildtype


title: ZKD_MUT1_input


title: MUT1_IP


title: W34/70 9.7 minimal medium rep 2


title: WT-ILC-28-2

value: Innate lymphoid cells


title: MUT2_IP


title: W34/70 9.7 Day4 rep 2

value: day 4


title: WT2_IP


title: WT3_IP


title: CSD_MUT3_input

value: CSD mutant


title: Input control DLD-1/STAG3

description: control

value: epithelial tumor cells DLD-1

value: colorectal adenocarcinoma


title: W34/70 9.7 Day4 rep 1


title: ZKD_MUT3_input


title: CSD_MUT2_input


title: RDseq, ent1, rep1

value: Schneider S2


title: W34/70 9.7 Day2 rep 3

value: day 2


title: CSD_MUT1_input


title: Input control-2 K562/STAG3

description: control

source_name: bone marrow

value: lymphoblast  tumor cells K-562

value: chronic myelogenous leukemia


title: W34/70 9.7 Day2 rep 2

value: W34/70 mutant strain


title: W34/70 9.7 Day4 rep 3


title: Input control RPE/STAG3

description: control

source_name: retina, eye

value: RPE epithelial cells immortalized with hTERT

value: pigmented epithelium


title: WT-ILC-24-2


title: CBS1538 11.1 minimal medium rep 3

value: CBS1538 mutant strain

value: minimal medium


title: CBS1538 11.1 minimal medium rep 2


title: MUT1_input

value: input

value: mutant

value: FLAG


title: WT-ILC-22-1

value: 8 weeks old

value: intestine of wildtype mouse

value: Innate lymphoid cells


title: WT-ILC-27-2


title: WT-ILC-25-2


title: WT-ILC-24-1


title: WT-ILC-20-1


title: Input control-1 K562/SMC1B

description: control


title: WT1_input

value: wildtype


title: CBS1538 11.1 minimal medium rep 1


title: WT-ILC-19-2


title: WT-ILC-30-2


title: MUT3_input


title: CBS1538 11.1 Day4 rep 3

value: day 4


title: WT3_input


title: S9A

first: Chi

last: Zhou

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

description: all.counts.exp.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal


title: MUT2_input


title: CBS1538 11.1 Day4 rep 1


title: KO2Poly

description: Polysome-associated RNA

data_processing:
Reads were psuedoaligned using Kallisto (v0.44.0) to human gene transcript annotations (hg38) to estimate transcript abundance.
Kallisto output was imported into R for use with DESeq2 (v1.24.0) to determine log2 fold change using a likelihood ratio test where crosslinked RNA fractions were normalized to inputs for each LIN28B protein expressed. We used a gene count cutoff of 5.
genome build: hg38
processed data files format and content: Text file containing DESeq2 output of polysome sequencing analysis. Comparison is polysome fractions normalized to total RNA input and subsequently compared between WT BE2C and LIN28B Knockout BE2C cells.  log2FC(WT/LIN28BKO) and statistics are shown. Data was filtered for protein coding genes as well as genes detected across multiple datasets reported in this manuscript.Additional processed file is normalized counts for each sample replicate.

source_name: BE2C cells

value: polysome

value: LIN28B knockout


title: Input control-1 K562/STAG3

description: control

value: lymphoblast  tumor cells K-562

value: chronic myelogenous leukemia


title: WT-ILC-23-2


title: KO3Poly

description: Polysome-associated RNA


title: Input control-2 K562/SMC1B

description: control


title: CBS1538 11.1 Day4 rep 2


title: CBS1538 11.1 Day2 rep 3

value: CBS1538 parental strain

value: day 2


title: WT2_input


title: W34/70 9.7 Day2 rep 1

value: W34/70 mutant strain


title: WT-ILC-2-2


title: WT-ILC-17-2


title: KO1Poly

description: Polysome-associated RNA


title: WT-ILC-16-2


title: S5A

description: all.counts.exp.txt


title: CBS1538 11.1 Day2 rep 2


title: CBS1538 11.1 Day2 rep 1


title: S8A

description: all.counts.exp.txt


title: S7A

description: all.counts.exp.txt


title: WT1Poly

description: Polysome-associated RNA


title: S4A

description: all.counts.exp.txt


title: WT-ILC-15-2


title: WT-ILC-14-2


title: WT-ILC-15-1


title: S6A

description: all.counts.exp.txt


title: WT-ILC-11-2


title: KO2


title: S9B

description: all.counts.exp.txt

value: Tumor


title: WT-ILC-1-2


title: WT-ILC-17-1


title: R9-ILC-8-1

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every cell

value: 3 weeks after transplantation

value: intestine of recipients


title: S8B

description: all.counts.exp.txt


title: S3A

description: all.counts.exp.txt


title: S6B

description: all.counts.exp.txt


title: WT2Poly

description: Polysome-associated RNA


title: R9-ILC-7-1


title: WT3Poly

description: Polysome-associated RNA


title: KO1

value: input


title: KO3


title: S4B

description: all.counts.exp.txt


title: S3B

description: all.counts.exp.txt


title: WT3


title: 2: A549 Ctrl-2

first: Xiaolin

last: Zhang

address: No.74 Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
Qualified libraries were sequenced using Illumina platform. The sequencing strategy was PE150.
Raw Reads were obtained from Illumina sequencing. Clean Reads were obtained through data processing such as removal of low-quality sequences and joint contamination. All subsequent analyses were based on Clean Reads.
FPKM (Trapnell, C. et al., 2010) is a very effective tool to quantitatively estimate gene expression values using RNA-seq technology. FPKM is an abbreviation for Fragments per Kilobase per Million Fragments, the number of Fragments per thousand bases that are derived from a specific gene. It is the most commonly used gene expression level estimation method that takes into account the sequencing depth and gene length effect on the count of Fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: Ctrl

growth_protocol: A549 cells were cultured in 1640 medium (with 10% serum)

extract_protocol:
Medium were removed, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were transfected with empty vector or Flag-ORF3,36h post transfection, cells were collected(two separate experiments)

tag: transfection

value: Control


title: S2B

description: all.counts.exp.txt


title: WT-ILC-14-1

value: 8 weeks old

value: intestine of wildtype mouse


title: S7B

description: all.counts.exp.txt


title: 4: A549 SARS-CoV-2 ORF3-2

source_name: SARS-CoV-2 ORF3

value: SARS-CoV-2 ORF3


title: S2A

description: all.counts.exp.txt


title: R9-ILC-41-1

value: Innate lymphoid cells


title: R9-ILC-4-1


title: WT2

value: wildtype


title: R9-ILC-5-1


title: R9-ILC-6-1


title: WT1


title: R9-ILC-9-1


title: R9-ILC-35-1


title: R9-ILC-42-1


title: 3: A549 SARS-CoV-2 ORF3-1


title: S5B

description: all.counts.exp.txt


title: Input control Monkey 1610

description: control

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were cleaned using fastp application (github..com/OpenGene/fastp.git) . Reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromosome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988.
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

organism: Macaca fascicularis

source_name: dissected testis

extract_protocol:
Testis fractionation: Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through two mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

value: testis

value: male germline cells


title: R9-ILC-34-1


title: 1: A549 Ctrl-1


title: R9-ILC-33-1


title: Denatured dermis_rep2

city: Changsha

first: Ran

middle: Yan

last: qin

address: xiangyalu street

institute: Central south university

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy9 respectively using Arraystar Super RNA labeling Kit.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and/or Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: IP RNA

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs."IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Collected samples are maintained in liquid nitrogen

extract_protocol: Total RNA extracted using Trizol reagent.The purity and amount of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

treatment_protocol: Grinded the tissue in liquid nitrogen

value: Denatured dermis

tag: gender

value: female

tag: age

value: 56 years old

value: skin

source_name: SUP RNA


title: Denatured dermis_rep3

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy10 respectively using Arraystar Super RNA labeling Kit.

value: male

value: 36 years old


title: Denatured dermis_rep1

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy8 respectively using Arraystar Super RNA labeling Kit.

value: 33 years old


title: Normal skin_rep5

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy7 respectively using Arraystar Super RNA labeling Kit.

value: Normal skin

value: 43 years old


title: Denatured dermis_rep4

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy11 respectively using Arraystar Super RNA labeling Kit.

value: 41 years old


title: Input control Monkey 38

description: control

tag: antibody


title: Normal skin_rep4

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy6 respectively using Arraystar Super RNA labeling Kit.

tag: condition


title: R9-ILC-36-1

value: 3 weeks after transplantation

value: intestine of recipients


title: Denatured dermis_rep5

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy12 respectively using Arraystar Super RNA labeling Kit.


title: Normal skin_rep3

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy5 respectively using Arraystar Super RNA labeling Kit.


title: R9-ILC-30-1


title: R9-ILC-29-1


title: Normal skin_rep1

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA labeling Kit.


title: MyglaSWRecB cells, PUUV, rep2

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_2

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Mus musculus GRCm38/mm10 genome using STAR 2.7.3a
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Mus musculus GRCm38/mm10 genome
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue; raw_counts.txt

organism: Myodes glareolus

source_name: MyglaSWRecB cells

growth_protocol: MyglaSWRecB cells were plated at 2.5x10e5 cells per well and infected 24h later

extract_protocol:
Cells were washed with PBS and incubated for 5 min at room temperature with 500 uL of Trizol (Tri Reagent, Sigma Aldrich) before addition of 150 uL of chloroform for 10 min and centrifugation at 4 °C for 10 min at 11000 rpm. The aqueous phase was recovered and precipitated with isopropanol. After centrifugation, the pellet is washed in 70% ethanol then suspended in 50 mL of RNAse free water.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded mRNA seq kit

treatment_protocol: Four wells were incubated either with PUUV or PHV at MOI 0.5 or left non-infected. RNA was prepared from cells at day 5 post infection.

value: kidney

value: MyglaSWRecB epithelial cells

tag: infection

value: Puumala virus (PUUV)


title: MyglaSWRecB cells, PUUV, rep1

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_1


title: R9-ILC-31-1

value: Innate lymphoid cells


title: MyglaSWRecB cells, PHV, rep4

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_4

value: Prospect Hill virus (PHV, New World)


title: R9-ILC-27-1


title: R9-ILC-32-1


title: MyglaSWRecB cells, PUUV, rep3

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_3


title: Normal skin_rep2

description: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy4 respectively using Arraystar Super RNA labeling Kit.


title: MyglaSWRecB cells, PHV, rep3

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_3


title: MyglaSWRecB cells, NI, rep4

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_4

value: non infected


title: Diplonema ChRO-seq rep 3

city: Ithaca

first: Charles

last: Danko

state: NY

address: 235 Hungerford Hill Rd

institute: Cornell University

data_processing:
In order to align leChRO-seq data, a publically available script was used (https://github.com/Danko-Lab/utils/tree/master/proseq).
The libraries were prepared by means of adapters containing a specific molecular identifier.
For these specific transcripts, PCR duplicates were removed using PRINSEQ lite.
The adapters were cut from the 3’ end of remaining reads using cutadapt with a 10% error rate.
Reads from this data were mapped using BWA to the mouse reference genome (mm10) in addition to a single copy of the Pol I ribosomal RNA transcription unit (GenBank ID #U13369.1).
The specific location of the RNA polymerase active site was described by means of a single base which denoted the 5’ end of the nascent RNA.
This information corresponded to the position of the 3’ end of each sequenced read. Mapped reads were converted to bigWig format using BedTools
Libraries were normalized using the following formula:
For pachynema: (bedGraph ÷ library size) (P  ÷ LZ),
where LZ and P represent the relative transcriptional activity of each stage
This formula was repeated for all prophase I substages.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: dREG peak call bed files
Library strategy: leChRO-seq

source_name: Prophase I substages

extract_protocol:
Prophase I substages were isolated using STAPUT. 10 million cells were used as input to extra total chromatin. Briefly, chromatin from enriched prophase I substages was mixed with 50 µl 2x run-on master mix (10 mM Tris-HCl pH 8.0, 5 mM MgCl2,1 mM DTT, 300 mM KCl, 10 mM Biotin-11-CTP (Perkin Elmer # NEL542001EA), 400 uM ATP (NEB N0450S), 0.8 uM CTP (NEB N0450S), 400 uM GTP (NEB N0450S), 400 uM UTP (NEB N0450S), 40 uM Biotin-11-CTP (Perkin Elmer # NEL542001EA), 40 units SUPERase in RNase Inhibitor (Life Technologies AM2694), and 1% Sarkosyl (Fischer Scientific #AC612075000). The run-on reaction was incubated at 37˚C for 5 minutes and then stopped by adding Trizol LS (Life Technologies 10296010). RNA was extracted by adding chloroform and precipitating the aqueous phase with GlycoBlue and ethanol. Unincorporated biotin nucleotides were removed with Micro Bio-Spin P-30 Gel Columns, Tris Buffer (RNase-free)  (Bio-Rad #7326250). Nascent RNA was purified by binding streptavidin beads (NEB S1421S) and washed as described by Mahat et al., 201663. The RNA was removed from beads by Trizol and then followed with the 3’ adapter ligation using T4 RNA Ligase 1 (NEB M0204L). After this, a second bead binding was performed followed by a 5’ de-capping using RppH (NEB M0356S). The 5’ end of the transcript was phosphorylated using PNK (NEB M0201L) and then purified with Trizol (Life Technologies 15596-026). After this, a 5’ adapter was ligated onto the RNA transcript using T4 RNA Ligase I (NEB M0204L), and a third bead binding was performed. RNA was purified again with a Trizol and ethanol extraction
A reverse transcription reaction was performed in order to generate cDNA using SuperScript IV Reverse Transcriptase (Life Technologies 18090010). The cDNA was amplified with Q5 High-Fidelity DNA Polymerase (NEB M0491L) in order to generate the leChRO-seq libraries which were prepared using manufacturer’s protocol (Illumina) and single-end sequenced by means of Illumina NextSeq500 at Cornell University Biotechnology Resource Center.

value: Prophase I substages

value: Diplonema

tag: genotype

value: WT


title: Diplonema ChRO-seq rep 1


title: MyglaSWRecB cells, NI, rep3

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_3


title: Diplonema ChRO-seq rep 4


title: R9-ILC-23-1


title: R9-ILC-28-1


title: MyglaSWRecB cells, PHV, rep2

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_2


title: MyglaSWRecB cells, PUUV, rep4

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
B-PUUV_vs_C-NI_degs_DESeq2.csv
PUUV_4


title: R9-ILC-21-1


title: Pachynema ChRO-seq rep 3

value: Pachynema


title: MyglaSWRecB cells, NI, rep1

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_1


title: Diplonema ChRO-seq rep 2


title: R9-ILC-26-1


title: R9-ILC-25-1


title: R9-ILC-24-1


title: Leptonema/Zygonema ChRO-seq rep 4

value: Leptonema/Zygonema


title: MIA PaCa-2, L-Gln 40mM, Gem 0.5 uM, 48h [MP2_D_1]

city: Los Angeles

first: Carlos

middle: David

last: Cruz

state: California

address: 8700 Beverly Boulevard

department: SOCC

institute: Cedars Sinai

data_processing:
The read counts were normalized using the Trimmed Mean of the M-values (TMM) method and differential expression analysis was performed using integrated hypothesis testing method
Assembly: NOT PROVIDED
Supplementary files format and content: normalized values for each Sample

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 were cultured in RPMI-1640.

extract_protocol:
Total RNA was extracted and prepared using the RNeasy Mini extraction kit (Qiagen, Germantown, MA) according to the manufacturer’s instructions
Performed by Novogene company

treatment_protocol: Gln studies were performed in Gln-free RPMI 1640 supplemented with indicated concentrations of L-Gln and/or D-Gln

value: MIA PaCa-2

value: Pancreatic cancer cell line

value: L-Glutamine, Gemcitabine


title: MIA PaCa-2, L-Gln 40mM, Gem 0.5 uM, 48h [MP2_D_2]


title: Pachynema ChRO-seq rep 2


title: MIA PaCa-2, L-Gln 40mM, Gem 0.5 uM, 48h [MP2_D_3]


title: MyglaSWRecB cells, PHV, rep1

description:
A-PHV_vs_B-PUUV_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
PHV_1


title: Pachynema ChRO-seq rep 4


title: Leptonema/Zygonema ChRO-seq rep 3


title: MyglaSWRecB cells, NI, rep2

description:
B-PUUV_vs_C-NI_degs_DESeq2.csv
A-PHV_vs_C-NI_degs_DESeq2.csv
NI_2


title: MIA PaCa-2, L-Gln 40mM, Gem 0, 48h [MP2_C_2]

value: L-Glutamine


title: R9-ILC-20-1

value: 3 weeks after transplantation


title: R9-ILC-19-1

value: intestine of recipients


title: MIA PaCa-2, L-Gln 40mM, Gem 0, 48h [MP2_C_3]


title: Leptonema/Zygonema ChRO-seq rep 2


title: purE-3-1

city: xuzhou

first: zuobin

last: zhu

address: tongshan road 209

institute: xuzhou medical university

description: purE.txt

data_processing:
The quality control (QC) of the raw reads is required to determine whether the sequencing data is suitable for subsequent analysis
the filtered clean reads are aligned to the reference sequence (NCBI: GCF_000002985.6_WBcel235).
The expression levels of genes were standardized by FPKM.
Assembly: Reference Genome Version: GCF_000002985.6_WBcel235
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Whole body

growth_protocol: Worms were grown at 20℃ on nematode growth media (NGM) plates

extract_protocol: Total RNA was extracted from the synchronized adult C. elegans using Trizol (Invitrogen, NO:15596026) according to the manufacturing instructions. RNA was qualified and quantified using NanoDrop bioanalyzer and Agilent 2100 (Thermo Fisher Scientific, USA).

treatment_protocol: Caenorhabditis elegans fed by E.coli. Larva stage 4 worms were transferred to NGM containing E.coli BW25113 or purE.

value: Whole body

value: fed E. coli mutant strain purE


title: R9-ILC-2-1


title: R9-ILC-22-1


title: R9-ILC-15-1


title: R9-ILC-17-1


title: purE-2-1

description: purE.txt


title: Pachynema ChRO-seq rep 1


title: BW25113-2-1

value: fed E. coli BW25113


title: BW25113-3-1


title: Leptonema/Zygonema ChRO-seq rep 1


title: Diplonema ATAC-seq rep 2

data_processing:
ATAC-seq sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 and filtered for uniquely mapping pairs with a custom python script
Duplicate and multiple aligning reads were removed from the analysis with picardtools v2.1.1 “MarkDuplicates.”
Mapped reads were converted to bigWig format using BedTools.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
In order to prepare nuclei, 50,000 cells isolated by FACS were spun at 500g for 5 minutes immediately after sorting, followed by a wash using 50µl of cold 1 x PBS and centrifugation at 500g for 5 minutes. Cells were then lysed using a cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% IPEGAL CA-630). Immediately following lysis, nuclei were spun at 500g for 10 minutes in a refrigerated centrifuge. In order to avoid cell loss during nuclei preparation, a fixed-angle centrifuge was used and cells were carefully pipetted away from the pellet after centrifugation. Nuclei were stored at -80°C. Stored nuclei were thawed on ice and the pellet was resuspended in a transposase reaction mixture (25µl 2 x TD buffer, 2.5µl transposase (Illumina) and 22.5µl nuclease-free water). The transposition reaction mixture was carried out for 30 minutes at 37˚C. Immediately following transposition, the sample was purified by means of a Qiagen MinElute kit.
After purification, the library of fragments was amplified using 1 x NEBnext PCR master mix and 1.25µM of custom Nextera PCR primers 1 and 2 (Supplementary Table x).  The following PCR conditions were utilized: 72˚C for 5 minutes; 98˚C for 30 seconds; and thermocycling at 98˚C for 10 seconds, 63˚C for 30 seconds, and 72˚C for 1 minute. In order to reduce GC and size bias in the PCR analysis, PCR reactions were monitored using qPCR in order to stop amplification prior to saturation. This was done by amplification of the full libraries for five cycles, after which an aliquot of the PCR reaction was taken and 10µl of the PCR cocktail containing Sybr Green at a final concentration of 0.6x was added. This reaction was run for 20 cycles in order to determine the additional necessary number of cycles for the remaining 45µl reaction. The libraries were purified by means of a Qiagen PCR cleanup kit that yielded a final library concentration of ~30nM in 20µl. These libraries were amplified for a total of 10-12 cycles in order to generate the ATAC-seq libraries, which were prepared using the manufacturer's protocol (Illumina) and paired-end sequenced by means of Illumina NextSeq500 at Cornell University Biotechnology Resource Center.

tag: developmental stage


title: MIA PaCa-2, L-Gln 40mM, Gem 0, 48h [MP2_C_1]


title: R9-ILC-14-1

value: Innate lymphoid cells


title: R9-ILC-13-1


title: MIA PaCa-2, L-Gln 2mM, Gem 0.5 uM, 48h [MP2_B_2]


title: BW25113-1-1


title: Diplonema ATAC-seq rep 1


title: Pachynema ATAC-seq rep 2


title: MIA PaCa-2, L-Gln 2mM, Gem 0.5 uM, 48h [MP2_B_3]


title: Pachynema ATAC-seq rep 1


title: purE-1-1

description: purE.txt


title: MIA PaCa-2, L-Gln 2mM, Gem 0, 48h [MP2_A_3]


title: MIA PaCa-2, L-Gln 2mM, Gem 0.5 uM, 48h [MP2_B_1]


title: R9-ILC-11-1


title: mbf1c_NonA_Exp1

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

data_processing:
mapping: Read mapping was performed using STAR v2.6.0c against the A. thaliana reference genome Col-0, release Ensembl39 based on TAIR10 version 39, which included the Araport11 annotation.
read normalization: Raw counts were extracted from the STAR ReadsPerGene output files and filtered by removing lowly expressed genes with a sum smaller than 10 counts per gene across all conditions. The RNA-Seq counts were normalized by the method included in the DESeq2 package
Genome_build: EnsemblPlants version 39 of Arabidopsis thaliana
Supplementary_files_format_and_content: Default STAR output files (ASCII format): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

source_name: whole rosettes

growth_protocol: Plant lines were grown on soil in a climate chamber with 20°C day-time temperature and 6°C night-time temperature with a light intensity of 180 µE m-2 s-1 in a 14 h light cycle and a humidity of 60% at day and 70% at night. Plants were moved to a short day-climate chamber after one week of growth with the following conditions: 20°C/16°C day/night, 60%/75% humidity day/night, 8 h day length with 180 µE m-2 s-1. The plants were kept under short-day conditions for one week of short-day before being pricked (10 plants in one 10 cm pot). After pricking plants were grown one further week at short-day conditions and then transferred to long-day conditions (20°C day and 16°C night temperature with a day length of 16 h at a light intensity of 200 μE m-2 s-1).

extract_protocol:
Total RNA was isolated by a "single-step" Trizol based method. DNAse treatment was carried out on 4 µg of RNA and the removal of DNA was validated by qPCR using intron-specific primers. RNA integrity was validated by an Agilent 2100 Bioanalyzer.
Library preparation and RNA sequencing (RNA-Seq) was carried out at BGI Genomics and performed according to the BGISEQ-500 workflow.

treatment_protocol: 28 days old Arabidopsis rosettes were used for cold acclimation and deacclimation experiments. For cold acclimation, plants were transferred to 4°C for 3 days with light intensity of 90 µE m-2 s-1 and 16 h day length and humidity of 70-80%. For deacclimation plants were moved back to long-day conditions for up to 4 days. Arabidopsis rosettes were harvested before (NonA) or after cold acclimation (ACC) either and for deacclimation either daily with an even tighter time course in the first 24 h (Deacc2h to Deacc96h) or after two (Deacc2) or four days (Deacc4) of deacclimation as shown in Figure 1 and frozen immediately in liquid nitrogen.

value: NonA

tag: plant line

tag: replicate

value: whole rosettes


title: Leptonema/Zygonema ATAC-seq rep 1

value: Prophase I substages


title: Leptonema/Zygonema ATAC-seq rep 2


title: Col0_ACC_Exp1

value: ACC


title: R9-ILC-10-1


title: R9-ILC-1-1


title: jub1_NonA_Exp1


title: MIA PaCa-2, L-Gln 2mM, Gem 0, 48h [MP2_A_1]

value: WT


title: MIA PaCa-2, L-Gln 2mM, Gem 0, 48h [MP2_A_2]


title: Col0_NonA_Exp1


title: R9-ILC-9


title: R9-ILC-12-1


title: jub1_Deacc4_Exp3


title: Diplonema RNA-seq rep 2

data_processing:
Reads were trimmed for low quality and adaptor sequences with cutadapt v1.8; parameters: -m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG --match-read-wildcards.
Reads were mapped to the reference genome (mm10.rRNA.fa.gz) using STAR v2.5.3a
Mapped reads were converted to bigWig format using BedTools.
To normalize for sequencing depth, libraries were scaled using reads per kilobase per million mapped reads (RPKM).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Prophase I substages were isolated using STAPUT. 1 million cells were used as input to extra total RNA. Immediately following STAPUT, testicular cells were lysed with TrizolLS (Thermo Fisher). Total RNA was purified using TrizolLS according to the commercial protocol with the following additions: after the first phase separation, an additional chloroform extraction step of the aqueous layer was performed using Phase-lock Gel heavy tubes (Quanta Biosciences); addition of 1ul Glyco-blue (Thermo Fisher) immediately prior to isopropanol precipitation; two washes of the RNA pellet with 75% ethanol. If the RNA integrity results indicated co-purified genomic DNA, it was removed with the RapidOUT DNA Removal kit (Thermo Fisher). RNA sample quality was confirmed by spectrophotometry (Nanodrop) to determine concentration and chemical purity (A260/230 and A260/280 ratios) and with a Fragment Analyzer (Advanced Analytical) to determine RNA integrity.
PolyA+ RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit 2.0 (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Advanced Analytical) prior to pooling. Libraries were sequenced on a NextSeq500 instrument (Illumina). At least 20M single-end 75bp reads were generated per library.

value: Diplonema


title: R9-ILC-8


title: mbf1c_Deacc4_Exp3


title: Pooled LMO library for 8 lung organoids_2

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

description:
MultiSeq Barcode map: MultiSeq-Barcode13=2478_Mock,MultiSeq-Barcode14=2478_SARS_CoV_2,MultiSeq-Barcode15=2522_Mock,MultiSeq-Barcode16=2522_SARS_CoV_2,MultiSeq-Barcode17=2524_Mock,MultiSeq-Barcode18=2524_SARS_CoV_2,MultiSeq-Barcode19=Lung_7_Mock,MultiSeq-Barcode20=Lung_7_SARS_CoV_2
roose-2_MSQ

library_source: other

data_processing:
sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 4.0.0) command with default parameters.
Gene expression fastq files were aligned to the Human  reference genome (with ENSEMBL v85 annotation), and MultiSeq Barcoding fastqs were counted against a reference of all possible MultiSeq barcodes using cellranger count (cellranger version 4.0.0) and default parameters.
MultiSeq Barcoding fastqs were counted against a reference of all possible MultiSeq barcodes using cellranger count (cellranger version 4.0.0).
Assembly: GRCH38.p7
Supplementary files format and content: H5ad formatted raw feature-barcode matrices produced by cellranger

molecule: other

source_name: lung

growth_protocol: Lung organoids were generated from lung ressections using the protocol described in Sachs et al, 2019

extract_protocol:
For the single-cell RNA sequencing experiments each organoid was generated from 4 different donors. After organoid dissociation into single-cell suspension using TrypLE express (ThermoFisher Scientific Cat#12604012), cells were counted, and pooled together (78,000 total cells).
Pooled cells were then loaded evenly across two lanes in the Chromium Controller for generating single-cell contained in lipid droplets following the manufacturer’s instructions (10X Genomics). A Chromium Single cell 3’ Reagent Kit (v3.1) (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries following the manufacturer’s instructions. All samples were encapsulated, and cDNA was generated within 6 hours after organoid processing. MULTISeq barcode libraries were generated using the protocol describedin Mcginnis et.al, Nature Methods (2019). Finally, Pooled libraries were sequenced on an Illumina NovaSeq 6000.
roose-1/2_GEX: 10X 3' Gene Expression; roose-1/2_MSQ: MULTI-Seq tagging of Single Cells using Lipid Barcodes

treatment_protocol: Lung organoids were removed from Matrigel following 1 minute incubation with Dispase 0.5U/ml (StemCell Technologies, Cat #07913), carefully transferred into a 15 ml tube, washed with DPBS (UCSF Cell Culture Facility) supplemented with 5 mm EDTA (Cellgro, Cat#46-034-CI) and pelleted (200g, 3 minutes at Room Temperature). Organoid pellets were resuspended in 500 µl of lung organoid media. Virus was added at MOI=0.15 for H1N1/PR8 mCherry and MOI=0.3 for SARS-CoV-2. Every organoid well contained 10,000 cells. After 2 hours of incubation, lung organoids were washed twice with PBS and resuspended in 300μL Matrigel (Corning) and plated in ~50 μL droplets in a 24 well tissue culture plate. Plates were placed at 37 degrees Celsius with 5% CO2 for 20 min to solidify the Matrigel droplets upon which 550uL of lung organoid media was added to each well. Plates were incubated in the standard tissue culture incubator at 37 degrees Celsius for 92 hours.

value: lung

tag: model

value: organoid

value: 4 mock + 4 infected with SARS-SoV-2


title: R9-ILC-7

tag: tissue


title: Diplonema RNA-seq rep 3


title: Pooled GEX library for 8 lung organoids_1

description:
processed data file contains LMO counts from roose-1_MSQ
roose-1_GEX

library_source: transcriptomic single cell


title: Diplonema RNA-seq rep 1


title: R9-ILC-5


title: jub1_Deacc2_Exp3


title: Healthy donor 3-isotype control mAb treatment [HD3_isotype]

city: Southampton

first: Aymen

last: Al-Shamkhani

address: Tremona Road

department: School of Cancer Sciences

institute: University of Southampton

data_processing:
Quality control analysis of the RNA-Seq data was conducted using FastQC
Alignment: Sequenced reads from each sample and run were aligned to the human genome (primary assembly, GRCh38.p12, GCA_000001405.27) using the STAR alignment algorithm (version 2.5.2b, default parameters).
Counts: Uniquely-mapped alignments overlapping gene exons were counted using feature Counts from the Rsubread package (version 1.32.4). Counting was performed relative to Ensembl 97 (Jul 2019) gene annotation and counts summarized at the gene level. Rsubread parameters: countMultiMappingRead=FALSE, isPairedEnd=TRUE.
Genome_build: GRCh38.p12, GCA_000001405.27
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini kit. The purity, concentration and integrity of the RNA were assessed using a Nanodrop Spectrophotometer (Thermo Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T cells

value: isotype control mAb

tag: subject status/id

value: Healthy donor 3


title: Pachynema RNA-seq rep 2

value: Pachynema