title: 12,13-diHOME, 24Hr, Donor B


title: Micorwell-seq datasets of Zebrafish_72hpf_COL85

status: Public on Jul 08 2022

type: SRA

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

library_source: transcriptomic

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For raw file in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp).
scRNA-seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Danio rerio GRCz11
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

molecule: polyA RNA

organism: Danio rerio

extract_protocol:
Whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

value: AB

tag: age

value: 72 hours

tag: tissue

value: whole organism


title: female_saline_D1_FosB_rep3

city: New York

first: Eric

middle: J.

last: Nestler

state: NY

address: 1425 Madison Ave L10-26

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
FS3D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

library_source: genomic

data_processing:
The NGS-Data-Charmer pipeline (Github commit date: June 18, 2020) was used for preprocessing, QC, and alignment of the dataset. Read alignment was performed with Bowtie2 (v2.4.1) (--dovetail --phred33) to the mm10 genome. Duplicated read pairs were subsequently removed using the samtools (v1.10) ‘rmdup’ module.
For generating combined bigwig files, bam files were merge using samtools  ‘merge’ module and corresponding index files were created using samtools ‘index’ module; bigwig files were then generated using Deeptools ‘bamCoverage’ module (bamCoverage --extendReads --ignoreDuplicates --centerReads --normalizeUsing CPM --binSize 10)
For each biological replicate and corresponding IgG control, peaks were called with MACS2 (v2.2.6) (macs2 callpeak -f BAMPE --pvalue 0.05 --keep-dup) and filtered through Irreproducible Discovery Rate (IDR) (v2.0.4.2) using 1% IDR threshold for bulk NAc datasets and 5% IDR threshold for NAc D1- and D2-MSN datasets. IDR output for each group were combined with Bedtools41 (v2.29.2) ‘merge’ module and the output containing high confidence peaks were utilized for further analysis.
Supplementary_files_format_and_content: combined bigwig files
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Mus musculus

source_name: nucleus accumbens

extract_protocol:
Nuclei were prepared through discontinuous sucrose gradient centrifugation, isolated through INTACT approach, and subject to CUT&RUN procedures.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacture instructions.

treatment_protocol: For IP-injection, animals received consecutive 7-day saline or cocaine injection. For self-administration, animals underwent 10-day 2hr per day introvenous self-administration.

tag: genotype

value: wild-type

tag: cell type

tag: Sex

value: male

tag: treatment

value: saline

tag: antibody

value: FosB (2251, Cell Signaling)

tag: administration

value: IP-injection


title: 12,13-diHOME, 24Hr, Donor A

city: San Francisco

first: Din

last: Lin

state: California

address: 513 Parnassus Ave.

institute: University of California, San Francisco

data_processing:
Quality control was performed using FASTQC v0.11.3 and quality trimming and adapter filtering with Trimmomatic v0.33 (Bolger et al., 2014)
The data in fastq format were mapped to human GRCh38
Gene list annotations were based on ensembl_hg_100 for human
RNA-seq datasets, raw read counts were converted to cpm using the edgeR package in R (www.R-project.org)
Assembly: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: Primary macrophage

extract_protocol:
RNA was harvested using RNAqueousTM-Micro Kit (Thermo Fisher Scientific). 4 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Preparation Kit (Illumina) following manufacturer's protocols.

value: Primary macrophage

value: WT

tag: time

tag: individual

value: donor A


title: TL_MOLM14_UT_unlab

city: Orange

first: Matthew

middle: D

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
library strategy: TimeLapse-seq (TL-seq)
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For TL-seq, reads were aligned to the GRCh38 genome using HISAT-3N aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Assembly: GRCh38
Supplementary files format and content: tdf

source_name: MOLM-14 cells

growth_protocol: MOLM-14 cells were cultured in RPMI (ATCC 30-2001) supplemented with 10% fetal bovine serum (Biological Industries; cat. No. S1480) and 1% Pen/Strep (ThermoFisher; cat. no. 15140122).

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq (TL-seq) genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TimeLapse-seq RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry using mCPBA as the oxidant as described in Schofield et al. Nature Methods 2018.
TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: MOLM-14 cells were treated with 1 µM JCS-1, JCS-2, RG3039, or DMSO for 6 hours,  and/or 100 µM s4U for 120 minutes. In all cases the s4U labeling was the last 120 minutes of small molecule treatment.

tag: cell line

value: none; untreated

tag: s4u feed

value: No


title: female_saline_D1_FosB_rep2

description:
FS2D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Micorwell-seq datasets of Zebrafish_72hpf_COL84


title: Micorwell-seq datasets of Zebrafish_72hpf_COL83


title: female_saline_D1_FosB_rep1

description:
FS1D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: male_cocaine_D2_FosB_control_rep3

description:
MC3D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: IgG (2729, Cell Signaling)


title: Vehicle, donor D

data_processing:
After removing Nextera adaptors using Trimmomatic v0.36, 50 bp paired-end reads were aligned to the human genome (hg19) using Bowtie2 v2.3.4.3.
After filtering reads from the mitochondrial genome and from unmapped contigs, paired reads with high mapping quality (MAPQ score > 10) were retained using SAMTools v1.10.
Duplicate reads were removed using the MarkDuplicates program, as implemented in Picard v2.18.29 (https://broadinstitute.github.io/picard/).
ATAC-seq peak regions for each sample were called using MACS2 v2.1.0 with parameters –nomodel –shift -100 -extsize 200.
Blacklisted regions from ENCODE were also excluded from called peaks (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability).
Assembly: hg19

extract_protocol:
Immediately after lysis, nuclei were spun at 500g for 10 minutes at 4°C
Resuspended the nuclei with Tn5 transposase reaction mix (25 µl 2X TD buffer, 2.5 µl Tn5 transposase, and 22.5 µl nuclease-free water) (Illumina Inc). The transposition reaction was performed at 37°C for 30 minutes. Immediately after the transposition reaction, DNA was purified using ZYMO DNA Clean & Concentrator kit.
Indexed libraries were generated using NEBNext® High-Fidelity DNA library prep PCR mix (New England Biolabs) and sequenced on an Illumina NovaSeq

value: Vehicle

value: donor D


title: Micorwell-seq datasets of Zebrafish_72hpf_COL82

value: AB


title: Micorwell-seq datasets of Zebrafish_72hpf_COL81

value: 72 hours


title: 12,13-diHOME 50uM, donor D

value: 12,13-diHOME 50uM


title: LPS 100ng/mL, donor C

value: LPS 100ng/mL

value: donor C


title: male_cocaine_D2_FosB_control_rep2

description:
MC2D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: male


title: Microwell-seq datasets of Zebrafish_3m_COL128

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For raw file 1-5 in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp). For raw file 6 in each COL, cellbarcode: in read1, the bases 1-6, 7-12, 13-18 are merged (18bp); UMI: in read1, the bases 19-24 (6bp).
scRNA-seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Danio rerio GRCz11
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

value: 3 month (90 day)

value: whole organism


title: male_cocaine_D2_FosB_control_rep1

description:
MC1D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: TL_MOLM14_JCS1_1

value: WT

value: Yes


title: male_cocaine_D1_FosB_control_rep3

description:
MC3D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Micorwell-seq datasets of Zebrafish_72hpf_COL86


title: male_cocaine_D1_FosB_control_rep2

description:
MC2D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: 12,13-diHOME 50uM, donor C

value: Primary macrophage


title: Microwell-seq datasets of Zebrafish_3m_COL127


title: LPS 100ng/mL, donor B

value: donor B


title: 12,13-diHOME 50uM, donor B


title: male_cocaine_D1_FosB_control_rep1

description:
MC1D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: IgG (2729, Cell Signaling)


title: LPS 100ng/mL, donor D

value: donor D


title: male_saline_D2_FosB_control_rep3

description:
MS3D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: Microwell-seq datasets of Zebrafish_3m_COL126

value: AB


title: Vehicle, donor B

value: Vehicle


title: Microwell-seq datasets of Zebrafish_3m_COL124


title: LPS 100ng/mL, donor A

value: LPS 100ng/mL

value: donor A


title: male_saline_D2_FosB_control_rep2

description:
MS2D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: 12,13-diHOME 50uM, donor A

value: 12,13-diHOME 50uM


title: male_saline_D2_FosB_control_rep1

description:
MS1D2C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: Microwell-seq datasets of Zebrafish_3m_COL123

value: 3 month (90 day)

value: whole organism


title: Microwell-seq datasets of Zebrafish_3m_COL122


title: Vehicle, donor A

value: WT


title: Microwell-seq datasets of Zebrafish_3m_COL121


title: male_saline_D1_FosB_control_rep2

description:
MS2D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: Microwell-seq datasets of Zebrafish_3m_COL100


title: Vehicle, donor C

value: Primary macrophage

value: donor C


title: male_saline_D1_FosB_control_rep3

description:
MS3D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: GSK3kd_CHIR_1

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description: bulk polyA RNA

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to process raw single-cell sequencing data with the GRCh38 reference. For infected samples, we used GRCh38 augmented by the IAV (DQ487333.1) genome.
We used CellBender (Fleming et al., 2019) to remove background RNA and scrublet (Wolock et al., 2019) to identify doublets.
Single-cell RNA sequencing data analysis was performed in R (version 4.0.3) with Seurat (version 4.0.1). Cells with at least 500 but less than 5000 detected genes, less than 25000 UMIs and less than 10% mitochondrial content were combined from each library and library depth (total number of UMIs) and cell cycle score was regressed out when scaling data. We then integrated samples using ‘IntegrateData’
Bulk RNAseq reads were mapped against GRCh38 using STAR (version 2.7.3a)
Bulk RNAseq gene expression was quantified with featureCounts (version 2.0.0) using the Gencode v33 reference
Genome_build: GRCh38

growth_protocol: After thorough washing with HBSS, the lung tissue tissue was minced with scissors and transferred to an enzyme mixture containing 500 U/mL Collagenase I (Gibco), 5 U/mL Dispase II (Gibco), and 1 U/mL DNase (Applichem) in HBSS supplemented with 10 µM Y-27632 dihydrochloride (Tocris) (36). The minced tissue was incubated for 45-60 min in a shaking water bath at 37°C before being vigorously vortexed and passed through a sieve to remove undigested tissue pieces.  Cells were centrifuged (300 x g, 5 min), resuspended in red blood cell (RBC) lysis buffer (Invitrogen), and incubated for 5 min at RT to remove erythrocytes. Subsequently, cells were washed with ADF++ (Advanced DMEM/F12 (Invitrogen) with 10 mM HEPES (Invitrogen) and 1x GlutaMax (Invitrogen)), counted, and seeded in the extracellular matrix substitute Cultrex (R&D) at a concentration of ~2000 cells/µL. Upon solidification of the gelatinous matrix, the following medium, adapted from (7), was added on top of the cultures to induce growth of lung organoids: ADF++ supplemented with 10 % R-spondin1 conditioned medium (produced as described previously (37) using the 293T HA Rspo1‐Fc cell line), 1x B27 supplement (Invitrogen), 1x Primocin antibiotic mix (Invivogen), 1.25 mM N-Acetylcysteine (Sigma), 5 mM Nicotinamide (Sigma), 0.5 µM SB202190 (Sigma), 1 µM A83-01 (Merck), 100 ng/µl human Noggin (Peprotech), 100 ng/µl human FGF10 (Peprotech) and 25 ng/ml human FGF7 (Peprotech). Y-27632 dihydrochloride (10 µM, Tocris) was added only in the first week of culture (7). The GSK-3 inhibitor CHIR-99021 (Sigma, 3 µM) as well as the SHH inhibitor Vismodegib (Selleckchem, 10 µM) and the NOTCH inhibitor DAPT (Sigma, 10 µM) were added to the cultures as indicated.  Organoids were kept in an incubator at 37°C, 5 % CO2.

extract_protocol:
Single cells were generated from organoids by enzymatic digestion with TrypLE Express enzyme (12-15 min, 37°C), followed by mechanical disruption through vigorous vortexing. Subsequently, cells were washed with ADF++, passed multiple times through a 27G needle, and filtered with a 40 µm strainer to remove any remaining cell clumps. To collect several samples for simultaneous scRNA-seq, some cells were exposed to methanol fixation (see Table S2). To this end, cells were washed twice by centrifugation (300xg, 5min) with 1 ml cold DPBS before being resuspended in 200 µl cold DPBS. Next, 800 µl ice-cold methanol was added dropwise to the cell suspension. The cells were then stored at -20°C and rehydrated shortly before scRNA-seq by equilibration to 4°C, centrifugation (1000xg, 5 min) and resuspension in rehydration buffer (0.04% BSA, 1 mM DTT, 0.2 U/µl RNase inhibitor in 3x SSC buffer (Sigma). Before performing scRNA-seq, fixed as well as fresh cells were diluted to a concentration of 10.000 cells/µl in rehydration buffer or ADF++, respectively. Upon growth, for 2-4 weeks organoids were expanded by enzymatic digestion. To this end, organoids were released from Cultrex with cold ADF++, centrifuged (300 x g, 5 min), incubated in TrypLE Express Enzyme (Gibco) for ~5-6 min at 37°C and briefly vortexed. After washing with ADF++, cells were resuspended in Cultrex at a ratio of 1:3 to 1:8.
For organoid as well as lung tissue samples single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3′ V3.1 library preparation kit according to the manufacturers’ instructions (10x Genomics). Full-length cDNA tagged with cell-barcode identifiers was PCR-amplified and sequencing libraries were prepared.
The constructed libraries were either sequenced on the Nextseq 500  using 28 cycles for read 1, 55 cycles for read 2, and 8 index cycles, or on the Novaseq 6000 S1 using 28 cycles for read 1, 64 cycles for read 2, and 8 index cycles, to a median depth of 36000 reads per cell.

treatment_protocol: Mature human lung organoids were collected on ice to remove the remaining matrix and broken up by repeated resuspension using a disposable syringe with 27G needle. Before infection one organoid well was dissociated into single cells (as described above) to determine the cell number. Organoid fragments were then either mock-infected with infection medium (ADF++) or challenged with influenza A virus (MOI 0.4) for 1 h at RT. After infection, organoids were washed with ADF++, resuspended in Cultrex and overlaid with the respective organoid medium (as described above). Samples for scRNA-seq and IAV replication were taken at indicated time points. To ensure retrieval of all infectious particles generated within a given time in the culture, the gelatinous matrix was dissolved by pipetting up and down with the overlaid medium. Then the mixture of medium, matrix and organoids was incubated for 5 min on ice and centrifuged (300xg, 5 min). The supernatant was transferred to new tubes and frozen at -80°C.

value: alveolar organoid

tag: batch


title: ctrl_ctrl_1

description: bulk polyA RNA


title: Microwell-seq datasets of Zebrafish_3m_COL98


title: male_saline_D1_FosB_control_rep1

description:
MS1D1C
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IgG (2729, Cell Signaling)


title: male_cocaine_D2_FosB_rep3

description:
MC3D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: cocaine

value: FosB (2251, Cell Signaling)


title: male_cocaine_D2_FosB_rep2

description:
MC2D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Zebrafish_3m_COL97

value: AB


title: GSK3kd_CHIR_2

description: bulk polyA RNA


title: Microwell-seq datasets of Zebrafish_3m_COL125


title: Microwell-seq datasets of Zebrafish_3m_COL99


title: GSK3kd_ctrl_2

description: bulk polyA RNA


title: male_cocaine_D2_FosB_rep1

description:
MC1D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: Microwell-seq datasets of Zebrafish_3m_COL96


title: male_cocaine_D1_FosB_rep3

description:
MC3D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: GSK3kd_ctrl_1

description: bulk polyA RNA


title: Microwell-seq datasets of Zebrafish_3m_COL95


title: Microwell-seq datasets of Zebrafish_3m_COL94


title: ctrl_CHIR_1

description: bulk polyA RNA


title: male_cocaine_D1_FosB_rep1

description:
MC1D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: ctrl_ctrl_2

description: bulk polyA RNA


title: male_cocaine_D1_FosB_rep2

description:
MC2D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.


title: AO37_HT280_Epcam

description:
single-cell polyA RNA
HT280_Epcam.rds

value: HT280+/Epcam+ cells

value: control


title: ctrl_CHIR_2

description: bulk polyA RNA


title: Microwell-seq datasets of Zebrafish_3m_COL92


title: male_saline_D2_FosB_rep2

description:
MS2D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: saline


title: Microwell-seq datasets of Zebrafish_3m_COL91


title: AO36_HT280_Epcam

description:
single-cell polyA RNA
HT280_Epcam.rds


title: male_saline_D2_FosB_rep1

description:
MS1D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type


title: AO34_HT280_Epcam

description:
single-cell polyA RNA
HT280_Epcam.rds


title: Microwell-seq datasets of Zebrafish_3m_COL90


title: AO22_pool_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds

value: bronchial organoid

value: IAV-infection


title: male_saline_D1_FosB_rep3

description:
MS3D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: male


title: AO23_HT280

description:
single-cell polyA RNA
HT280_Epcam.rds

value: HT280+ cells


title: Microwell-seq datasets of Zebrafish_3m_COL88

value: 3 month (90 day)

value: whole organism


title: Microwell-seq datasets of Zebrafish_3m_COL89


title: AO22_pool_16h_control

description:
single-cell polyA RNA
organoids_all.rds
organoids_pool.rds


title: AO22_HT280

description:
single-cell polyA RNA
HT280_Epcam.rds


title: Microwell-seq datasets of Zebrafish_3m_COL87


title: male_saline_D1_FosB_rep1

description:
MS1D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: IP-injection


title: Microwell-seq datasets of Zebrafish_3m_COL93


title: KO-H3K9me2

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
Library strategy: CUT&Tag
Raw paired-end sequenced reads were first cut adaptors and trimmed using trim_galore (v0.6.6) with “-q 20, --stringency 1, --length 20 and -e 0.1”.
Then, these cleaned fastq data were mapped using bowtie2 (v2.4.2) to the mm10 reference genome with “--end-to-end, --very-sensitive, --no-mixed, --no-discordant, --phred33, -I 10 and -X 700” model
Next, Picard was used for marking and removing duplication. Samtools (v1.11) was used for converting and sorting the sam files to sort bam files
Finally, Macs2 was used for peak calling with “-q 0.01, -–broad-cutoff 0.01, –-broad-cutoff –keep-dup all”. Differential peaks between WT and KO were calculated by homer mergePeaks and homer getDifferentialPeaks with “-F 2 -P 0.0001”.
Peaks were annotated by annotatePeaks.pl with mm10 genome and gencodeVM25 gtf files. Parallelly, deeptools was used for normalizing signals from sort bam files via bamCoverage with “-–RPKM”, computeMatrix was used for calculating the overall signal distribution around the peak center called by macs2 using “reference-point” model with “-b 2000, -a 2000, --missingDataAsZero, --referencePoint center, --skipZeros, --blackListFileName mm10.blacklist.bed (discarding weird regions)”. Data were visualized using plotProfile and plotHeatmap in deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: peak text file
Supplementary_files_format_and_content: bigwig file

source_name: Activated B cells

extract_protocol:
H3K9me2 modified genomic regions were harvested by anti-H3K9me2 antibody and “TD903 Hyperactive® Universal CUT&Tag Assay Kit for Illumina”
Libraries were constructing using “TD903 Hyperactive® Universal CUT&Tag Assay Kit for Illumina” and “TD202 TruePrep® Index Kit V2 for Illumina®” from Vazyme Biotech Co., Ltd

value: jmjd1c B KO

value: Activated B cells


title: Microwell-seq datasets of Zebrafish_3m_COL85


title: H1299 cells, PLVT7_CCNB1_3

city: Zunyi

first: Qing

last: Luo

state: Guizhou

address: 149 Dalian Road, Huichuan District, Zunyi, Guizhou 563003, P. R. China

institute: Affiliated Hospital of Zunyi Medical University

data_processing:
The original image data file obtained by Illumina NovaSeq recognition was transformed into the  original sequencing sequence (Sequenced Reads) base on the bcl2fastq v2.20 base recognition  (Base Calling) analysis
In order to guarantee the data quality which was used to analysis, the  useful Perl script was used to filter the original data (Raw Data). The steps are:  1)Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed  Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both  of the reads must be removed );  2)Remove the contaminated reads for adapters (The contaminated reads for  adapters was defined that the Read Bases contained more than 5bp of adapter  sequences. If either one of the PE Reads was polluted, we will remove both ends  of the reads);  3)Remove the low quality reads (The low quality reads was defined that the number  of Reads Bases whose phred Quality value was less than or equal to 19  accounted for more than 15% . If either one of the PE Reads defined as low  quality, we will remove both ends of the reads);  4)Remove the reads whose N base more than 5% for total bases (If either one of  the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by featureCounts(V2.0.3), and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes  (DEGs) by using DESeq2-a R package.
Assembly: Homo_sapiens.(GRCh38.p13)
Supplementary files format and content: counts table in xlsx format
Supplementary files format and content: FPKM table in xlsx format

source_name: lung adenocarcinoma

growth_protocol: H1299 mesenchymal cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNAiso plus kit (Takala).  total RNA was used for the construction of sequencing libraries.
Preparation of library by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and sequencing of transcriptome were implemented with Illumina NovaSeq 6000 system.

treatment_protocol: Screening of stable transfectants was induced by treatment of 14-day post confluent cells  with 1ug/ml puromycin.

value: lung adenocarcinoma

value: CCNB1 knockdown


title: AO22_HT2_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds

value: alveolar organoid


title: male_saline_D1_FosB_rep2

description:
MS2D1F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: FosB (2251, Cell Signaling)


title: H1299 cells, PLVT7_CCNB1_2


title: AO35_HT280_Epcam

description:
single-cell polyA RNA
HT280_Epcam.rds

value: HT280+/Epcam+ cells


title: Day 9-RA+BMP4

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Illumina Casava software used for basecalling.
10x Genomic Chromium mapping and analysis procedure
Cell Ranger v.3.0.2
Genome_build: Mouse GrCm38 genome
Supplementary_files_format_and_content: 10x Genomic Chromium expression files

source_name: differentiated neurons from mESCs at day 9

extract_protocol:
After a quick PBS wash at day 9 of the differentiation, cells were dissociated with 0.25% cold trypsin. Cells were pelleted and dead cells were removed using Dead Cell Removal Kit (MIltenyi Biotec). Live cells were counted using hemocytometer and resuspended in 0.04% BSA/PBS solution at 1000 cells/ ul density and library preparation and sequencing was perfomed following 10X genomics chromium protocols.
Single cell suspension from day 9 cultures were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, Pleasanton, CA) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on 1 lane of NovaSeq 6000 S2 flowcell at UCLA Technology Center for Genomics and Bioinformatics.

value: MM13 mESC line

tag: condition

value: under RA+BMP4 condition


title: Microwell-seq datasets of Zebrafish_3m_COL84

value: AB


title: male_saline_D2_FosB_rep3

description:
MS3D2F
Please use Processed_data_files_Key.xlsx file on the series record to map samples to associated processed data files.

value: wild-type

value: saline


title: H1299 cells, PLVT7_CCNB1_1


title: AO22_HT2_16h_control

description:
single-cell polyA RNA
organoids_all.rds

value: control


title: Microwell-seq datasets of Zebrafish_3m_COL83


title: Day 9-RA

value: under RA condition


title: AO18_pool_batch1_control

description:
single-cell polyA RNA
organoids_pool.rds

value: bronchial organoid


title: H1299 cells, PLVT7_MOCK_3

value: WT


title: Microwell-seq datasets of Zebrafish_3m_COL82

value: 3 month (90 day)

value: whole organism


title: Oxazolone ICOS FC

city: Montreal

first: Woong-Kyung

last: Suh

state: QC

address: 110 Pine avenue, SuhLab

country: Canada

institute: institut de Recherche Clinique de Montreal (IRCM)

data_processing:
The alignment of the reads was performed using Cellranger 4.0.0 (from 10x Genomics) with GRCm38.p6 (mm10) reference genome procured from Ensembl. The resulting expression matrix was loaded into R version 3.6.1 (from the R Foundation for Statistical Computing) to conduct analysis.
The expression matrices were stored into an R Seurat object available in the package Seurat version 3.0. For each condition (Steady state and Oxazolone), we filtered ICOS WT and ICOS FC samples by eliminating any cell that presented more than 10% mitochondrial RNA contamination as well as any cell with less than 200 unique genes expressed and we merged the ICOS FC and WT samples in each condition.
The expression matrix was then log normalized and scaled. The most differentially expressed genes within the samples were identified. As several cell cycle-related genes were identified, we used CellCycleScoring function available in Seurat to score cell cycle phases. After, we scaled the data by regressing cell cycle score variables (Phases S and G2/M) to minimize the importance of cell cycle genes.
We then proceeded with a dimensional reduction using a principal component analysis (PCA) approach based on the 2000 most variable features. We selected the first 30 most important eigenvectors produced by the PCA and constructed a Shared Nearest Neighbor (SNN) graph and we used Modularity Optimizer version 1.3.0  to identify 7 clusters for Steady state condition and 8 clusters for Oxazolone condition. The cells were projected on a 2D space using a Uniform Manifold Approximation and Projection UMAP method.
Genome_build: GRCm38.p6 (mm10) reference genome
Supplementary_files_format_and_content: Processed data: Rdata files
Supplementary_files_format_and_content: Expression matrix

source_name: T regulatory cells

extract_protocol:
Single cell suspensions were prepared from either spleens (for Steady state) or cervical draining LNs (for Oxazolone challenge day 1) from ICOS WT and ICOS FC mice.  Cells were stained with viability dye, anti-CD4 and anti-TCRβ. Live Treg (CD4+TCRβ+ YFP+) cells were sorted using a BD FACSAria (BD Biosciences) with more than 95% purity. A total of 12,000 cells from ICOS WT and ICOS FC mice were prepared for the library.
Libraries were generated at the IRCM Molecular Biology and Functional Genomics Core Facility using the following components from 10x Genomics: Chromium Next GEM Chip G Single Cell kit, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1, and Chromium i7 Multiplex kit.

value: cervical draining lymph nodes

value: Oxazolone

value: ICOS-deficient


title: H1299 cells, PLVT7_MOCK_2

value: lung adenocarcinoma


title: Microwell-seq datasets of Zebrafish_3m_COL86


title: AO16_pool_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds

value: IAV-infection


title: AO16_pool_16h_control


title: H1299 cells, PLVT7_MOCK_1


title: WT-H3K9me2

value: Activated B cells


title: Microwell-seq datasets of Zebrafish_3m_COL81


title: Oxazolone ICOS WT

value: ICOS WT


title: Microwell-seq datasets of Zebrafish_3m_COL80


title: Steady state ICOS WT

value: spleen

value: Steady state


title: AO16_HT2_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds

value: alveolar organoid


title: Steady state ICOS FC


title: A549 NIN KO, interferon, 24h, rep3

city: La Jolla

last: Daugherty

address: 9500 Gilman Drive

institute: University of California San Diego

description:
PE100 reads
Condition_NIN-KO_induced_vs_NIN-KO.csv
Condition_NIN-KO_induced_vs_WT_induced.csv

data_processing:
Resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina).
Sequencing reads were quantified with Salmon in a quasi-mapping-based mode to the reference genome
Files containing '100_u_IFNa' were replaced with 'induced.' Files containing 'Untreated' were replaced with 'uninduced'
Read quantifications were imported and differentially expressed genes across experimental conditions were identified using the R package DESeq2
Assembly: GRCh38.p13
Supplementary files format and content: DESeq2 formatted, comma-separated files.

growth_protocol: A549 cells (WT, NINL KO, NIN KO) were maintained in DMEM 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) and assessed for quality using an Agilent Tapestation 4200. Samples with a RIN larger than 8.0 were used to generate RNA sequencing libraries.
Libraries were generated using a TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina). Samples were processed according to manufacturer's instructions, starting with 500 ng of RNA and modifying shear time to five minutes.

treatment_protocol: "Interferon" cells were treated with 100 u recombinant human IFN alpha and harvested 24 hours post-treatment. "No treatment" cells were harvested at the same time as "interferon" cells.

value: epithelial cells

value: NIN KO

value: 100u IFN alpha


title: AO16_HT2_16h_control

description:
single-cell polyA RNA
organoids_all.rds

value: control


title: Microwell-seq datasets of Zebrafish_3m_COL79

value: AB


title: A549 NIN KO, interferon, 24h, rep2


title: AO15_pool_batch2_control

value: bronchial organoid


title: Microwell-seq datasets of Zebrafish_3m_COL77

value: 3 month (90 day)

value: whole organism


title: Microwell-seq datasets of Zebrafish_3m_COL78


title: A549 NIN KO, interferon, 24h, rep1


title: A549 NIN KO, no treatment, 24h, rep3

description:
PE100 reads
Condition_NIN-KO_vs_WT.csv
Condition_NINL-KO_vs_NIN-KO.csv
Condition_NIN-KO_induced_vs_NIN-KO.csv

value: no treatment


title: WT

first: Yuncai

last: Zhou

address: No. 818 Tianyuan East Road, Jiangning District

institute: Nanjing medical university

description: single cell total RNA

data_processing:
Illumina NovaSeq PE150 was used for sequencing and Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The quality control of our sequenced reads is as follows:  the first and last base mass of reads less than 3 will be removed. A group of 4 bases is taken as a group, if the average base mass of the group is less than 15, the sequence of this base group is removed.
The trimmed data was then mapped to mm10 whole genome using STAR_2.5.1b software and calibrated using the GTF annotation file to distinguish exon region, intron region and intergene regionreads. The discrimination rule was: reads were denoted as an exon region at least 50% sequence were matched, reads that were aligned to non-exons and intersected with the intron region were denoted as an intron region, otherwise were denoted as intergenomic regions.
Principal component analysis (PCA) was used to reduce the dimensionality of data sets, and transferred to  t-Stochastic Neighbor Embedding (t-SNE) by Cell Ranger 2.1.0 software.
Cell clustering and significant analysis of differentially expressed genes were accomplished by cell ranger 2.1.0 software.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger matrix

source_name: Islet

extract_protocol:
Islets were isolated and digested at 37°C for 5 min by 0.08 % trypsin containing 0.006 % EDTA to generate islet single cell, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/μl, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: islet

value: postnatal day 70

value: wild type


title: pho92_9H_R3

city: Illkirch

first: Jérémy

last: Scutenaire

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description:
50 nt read length
Table S1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the SK1 assembly of the Saccharomyces cerevisiae genome (SK1 MvO V1; SK1_SGD_2018_NCSL00000000) using Tophat 2.0.14 (Kim et al., 2013; Trapnell et al., 2009) and bowtie version 2-2.1.0 (Langmead et al., 2009). Only uniquely mapped reads have been retained for further analyses.
Quantification of gene expression has been performed with HTSeq-0.6.1 (Anders et al., 2015), using intersection-nonempty mode, and annotations coming from the Saccharomyces Genome Database (SGD). Only non-ambiguously assigned reads have been retained for further analyses.
Comparisons of interest have been performed using R 3.5.1 with DEseq2 version 1.22.1 (Love et al., 2014). More precisely, read counts were normalized from the estimated size factors using the median-of-ratios method (Anders and Huber, 2010) and a Wald test was used to estimate the p-values. P-values were then adjusted for multiple testing with the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
Assembly: SK1 MvO V1: SK1_SGD_2018_NCSL00000000
Supplementary files format and content: Table S1. Excel file for mRNA-seq data include for each detectable transcript: raw read count, normalized values, gene informations, log2foldchange expression value in mutants vs WT, p-value and adjusted p-value

organism: Saccharomyces cerevisiae

source_name: SK1 pCUP-IME1

growth_protocol: Synchronous meiotic entry was performed in standard procedure as described (Schwartz et al., 2013). Briefly, respiratory proficient diploids were pre-selected on 1% yeast extract, 2% peptone, 3% glycerol, 2% agar for 24 hr at 30°C, transferred for another 24 hr of growth in 1% yeast extract, 2% peptone, 4% dextrose at 30°C and 170 rpm, diluted in BYTA media (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 nM potassium phthalate) to OD600 = 0.2 and incubated for another 16 hr incubation at 30°C and 170 rpm. Next, cells were washed once with sterile milliQ water and resuspended in SPO medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30°C and 170 rpm. To induce IME1 in the pCUP-IME1 background, 50 μM of copper (II) Sulfate was added after 2 hr in SPO. Cells were isolated from SPO at the indicated time points by centrifugation (3 min at 8,000 g).

extract_protocol:
Total RNAs were extracted on 2.0 - 3.0 OD of 2 OD/ml yeast cells using a standard hot acid phenol protocol.
mRNA-seq libraries were generated from 500 ng of total RNA using TruSeq® Stranded mRNA Library Prep kit and TruSeq® RNA Single Indexes kits A and B (Illumina, Cat#20020595) according to manufacturer's instructions. Quantity and quality of the started material and final librairies were checked using a Qubit™ fluorometer (Invitrogen™) and Agilent Bioanalyzer. Resulting libraries were sequenced in 50-length Single-Read on a HiSeq 4000 machine (Illumina).

value: SK1 pCUP-IME1

value: diploid meiotic yeast

value: pho92 mutant


title: Microwell-seq datasets of Zebrafish_3m_COL76


title: A549 NIN KO, no treatment, 24h, rep2


title: A549 NIN KO, no treatment, 24h, rep1


title: AO15_HT2_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds

value: IAV-infection


title: Microwell-seq datasets of Zebrafish_3m_COL74


title: pho92_6H_R3

description:
50 nt read length
Table S1


title: A549 NINL KO, interferon, 24h, rep2

description:
PE100 reads
Condition_NINL-KO_induced_vs_WT_induced.csv
Condition_NINL-KO_induced_vs_NINL-KO.csv

value: NINL KO


title: A549 NINL KO, interferon, 24h, rep3

value: epithelial cells


title: pho92_5H_R3

description:
50 nt read length
Table S1


title: AO13_pool_batch2_control


title: βTG miR-503

description: single cell total RNA

value: Beta cell specific miR-503 transgenic


title: Microwell-seq datasets of Zebrafish_3m_COL75


title: pho92_3H_R3

description:
50 nt read length
Table S1


title: Microwell-seq datasets of Zebrafish_3m_COL73


title: pho92_2H_R3

description:
50 nt read length
Table S1


title: AO15_HT2_16h_control

description:
single-cell polyA RNA
organoids_all.rds
organoids_HT2.rds

value: alveolar organoid


title: AO15_pool_16h_H3N2

description:
single-cell polyA RNA
organoids_all.rds


title: Microwell-seq datasets of Zebrafish_3m_COL71


title: A549 NINL KO, interferon, 24h, rep1

value: 100u IFN alpha


title: Microwell-seq datasets of Zebrafish_3m_COL72

value: AB


title: PMP cells - E1

city: Piscataway

first: Mengmeng

last: Jin

state: NJ

address: 604 Allison Rd

institute: Rutgers University

data_processing:
Fastq files were generated using the Bcl2Fastq software, version 1.8.4.
The genome sequence was then indexed using the rsem-prepare-reference command. Each fastq file was trimmed using the fastp program (v0.12.2) and then aligned to the human genome (GRCh38/hg38) using HISAT2 (v.2.2.0).
Gene counts were extracted from bam files using Rsubread/featureCounts in R with a UCSC transcript map.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix

source_name: primitive macrophage progenitor

growth_protocol: The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months.

extract_protocol:
Total RNA was prepared with an RNAeasy kit (QIAGEN).
Libraries were constructed by using 600 ng of total RNA from each sample and utilizing a TruSeqV2 kit from Illumina (Illumina, San Diego, CA) following the manufacturer’s suggested protocol.

value: human iPSC derived primitive macrophage progenitors (PMPs)


title: Microwell-seq datasets of Zebrafish_3m_COL70

value: 3 month (90 day)


title: pho92_0h_R3

description:
50 nt read length
Table S1


title: AO13_pool_batch1_control

value: bronchial organoid

value: control


title: ime4_9H_R3

description:
50 nt read length
Table S1

value: ime4 mutant


title: A549 NINL KO, no treatment, 24h, rep2

description:
PE100 reads
Condition_NINL-KO_vs_WT.csv
Condition_NINL-KO_induced_vs_NINL-KO.csv
Condition_NINL-KO_vs_NIN-KO.csv

value: no treatment


title: PMP cells - C3


title: Microwell-seq datasets of Zebrafish_3m_COL69

value: whole organism


title: AO15_pool_16h_control


title: A549 NINL KO, no treatment, 24h, rep3


title: pho92_7H_R3

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1


title: PMP cells - B2


title: ime4_7H_R3

description:
50 nt read length
Table S1

value: diploid meiotic yeast


title: PMP cells - UTY1


title: ime4_5H_R3

description:
50 nt read length
Table S1


title: Microwell-seq datasets of Zebrafish_3m_COL68


title: A549 WT, interferon, 24h, rep1

description:
PE100 reads
Condition_WT_induced_vs_WT.csv
Condition_NINL-KO_induced_vs_WT_induced.csv
Condition_NIN-KO_induced_vs_WT_induced.csv

value: WT


title: A549 WT, interferon, 24h, rep2


title: A549 WT, interferon, 24h, rep3


title: PMP cells - C5


title: Microwell-seq datasets of Zebrafish_3m_COL67


title: ime4_3H_R3

description:
50 nt read length
Table S1


title: S18_TB-ORG-DIFF3 [V9.3]

city: Vienna

first: Martin

last: Knoefler

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
alignement to human reference genome GRCh38 with Gencode 29 annotations using STAR aligner (version 2.6.1a) in 2-pass mode
reads per gene were counted by STAR
isoforms were quantified and compared using RSEM/EBSeq
count matrices from the two batches were merged in R version 4.1.0 by ENSG
genes with reads below 50 in 90% of samples were filtered out
differential gene expression was calculated using DESeq2 version 1.22.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv file of merged count matrices of the two batches with ENSG annotation

source_name: extravillous trophoblasts isolated in-vitro from trophoblast organoids, cultured with recombinant TGFB1

growth_protocol: TB-ORG were cultivated in 60 % growth factor reduced Matrigel and 40 % advanced DMEM/HamF12 containing 1 x B27, 1 x ITSX, 2 mM Glutamine, 10 mM Hepes, 0.05 mg/ml gentamicin, 2 µM A8301, 50 ng/ml EGF, and 3 µM CHIR99021.

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Illumina RNA-Seq Library Preparation stranded RNA with poly-A enrichment (NEB Next Ultra II Directional RNA Library Prep Kit for  Illumina)
2x75bp Paired End Read; >50million read pairs per sample

treatment_protocol: TB-ORG-EVT differentiation was performed in advanced DMEM/HamF12 containing 1 x B27, 1 x ITSX, 2 mM Glutamine, 10 mM Hepes, 0.05 mg/ml gentamicin, 50 ng/ml EGF, and with or without 2 µM A8301, and with or without 5 ng/ml recombinant TGFb1.

tag: donor

tag: tissue of origin

value: trophoblast organoids

tag: gestational week

value: 7 - 8th week of gestation

tag: culture conditions

value: w/o TGFb-inhibitor

value: rec TGFB1

tag: sequencing batch

tag: in-situ/in-vitro

value: in-vitro


title: ime4_6H_R3

description:
50 nt read length
Table S1

tag: cell type

tag: genotype


title: Microwell-seq datasets of Zebrafish_3m_COL64

tag: strain

tag: age

tag: tissue


title: Microwell-seq datasets of Zebrafish_3m_COL66


title: Microwell-seq datasets of Zebrafish_3m_COL65


title: ime4_0h_R3

description:
50 nt read length
Table S1


title: PMP cells - ND20


title: ime4_2H_R3

description:
50 nt read length
Table S1


title: Microwell-seq datasets of Zebrafish_3m_COL63


title: WT_9H_R3

description:
50 nt read length
Table S1


title: WT_7H_R3

description:
50 nt read length
Table S1


title: A549 WT, no treatment, 24h, rep2

description:
PE100 reads
Condition_WT_induced_vs_WT.csv
Condition_NINL-KO_vs_WT.csv
Condition_NIN-KO_vs_WT.csv

value: epithelial cells

tag: treatment

tag: time


title: S15_TB-ORG-DIFF3 [V11.3]


title: Microwell-seq datasets of Zebrafish_3m_COL61

value: AB


title: S17_TB-ORG-DIFF2 [V9.2]

source_name: extravillous trophoblasts isolated in-vitro from trophoblast organoids, cultured without TBFB-inhibitor

value: w/o rec TGFB1


title: A549 WT, no treatment, 24h, rep1

tag: cell line


title: A549 NINL KO, no treatment, 24h, rep1

value: NINL KO


title: S16_TB-ORG-DIFF1 [V9.1]

source_name: extravillous trophoblasts isolated in-vitro from trophoblast organoids, cultured with TBFB-inhibitor

value: TGFb-inhibitor


title: Microwell-seq datasets of Zebrafish_3m_COL62

value: 3 month (90 day)


title: WT_6H_R3

description:
50 nt read length
Table S1


title: DCVC_F2

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
Raw fastq files were first examined using fastQC (version 0.11.5) (Andrews 2010), and reports generated for all 24 samples were collated using multiQC (version 0.9)
Mapped reads to the human reference genome (hg38) were done using the Spliced Transcripts Alignment to a Reference (STAR) (version 2.6.0c)
Following mapping, featureCounts (version 1.6.1) was used to quantify aligned reads mapping to exons.
Quantification output from featureCounts was read into R (version 3.6.0), and analyzed with the DESeq2 package (version 1.24.0)
Genome_build: hg38
Supplementary_files_format_and_content: matrix of normalized counts for each gene and sample

source_name: differentiated THP1 cell line

growth_protocol: THP-1 cells were obtained from American Type Culture Collection. THP-1 cells were cultured using standard procedures at 37 °C and 5% CO2 in RPMI 1640 media supplemented with 10% FBS and penicillin/streptomycin (pen/strep). 24-h  prior to treatment, cells were plated in 24-well plates at a concentration of approximately 2x105 cells/mL with 100 nM phorbol 12-myristate 13-acetone (PMA).

extract_protocol:
RNA was extracted from THP-1 cells  using the Quick-RNA MiniPrep kit and standard protocol (Zymo Research).
RNA library preparation was performed using poly-A selection.

treatment_protocol: Following differentiation with PMA cells were subsequently treated with medium only or DCVC (1, 5, or 10 μM) for another 24 h. After DCVC treatment, medium was changed and gram negative bacterial cell membrane component/ inflammation inducer lipopolysaccharide (LPS; 100 ng/mL) was added to selected wells for 4 h. Treatment conditions included: medium only (control), LPS (100 ng/mL), DCVC (1, 5, or 10μM), and DCVC (1, 5, or 10μM) + LPS (100 ng/mL).

value: DCVC


title: LPS_F4

value: LPS


title: Microwell-seq datasets of Zebrafish_3m_COL45

value: whole organism


title: WT_5H_R3

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1


title: S13_TB-ORG-DIFF1 [V11.1]


title: WT_3H_R3

description:
50 nt read length
Table S1

value: diploid meiotic yeast


title: DCVC_LPS_F3


title: Microwell-seq datasets of Zebrafish_3m_COL44


title: WT_2H_R3

description:
50 nt read length
Table S1

value: WT


title: S11_TB-ORG-DIFF2 [V10.2]

value: trophoblast organoids


title: S10_TB-ORG-DIFF1 [V10.1]

value: 7 - 8th week of gestation


title: S9_TB-ORG-EVT [MK06012]


title: A549 WT, no treatment, 24h, rep3

value: no treatment


title: S12_TB-ORG-DIFF3 [V10.3]

value: w/o TGFb-inhibitor

value: rec TGFB1


title: DCVC_LPS_E3


title: Microwell-seq datasets of Zebrafish_3m_COL43


title: LPS_E4


title: pho92_9H_R2

description:
50 nt read length
Table S1

value: pho92 mutant


title: Microwell-seq datasets of Zebrafish_3m_COL42

value: AB


title: Control_E1

value: Control


title: Control_F1


title: Microwell-seq datasets of Zebrafish_3m_COL38


title: LPS_D4


title: S14_TB-ORG-DIFF2 [V11.2]

value: w/o rec TGFB1

value: in-vitro


title: DCVC_E2


title: S7_pEVT [MK06010]

source_name: extravillous trophoblasts isolated in-situ from placental tissue

value: placenta

value: in-situ


title: DCVC_LPS_D3


title: Microwell-seq datasets of Zebrafish_3m_COL37

value: 3 month (90 day)


title: Microwell-seq datasets of Zebrafish_3m_COL41

value: whole organism


title: S6_TB-ORG-EVT [MK06009]

value: TGFb-inhibitor


title: DCVC_D2

value: DCVC


title: S4_pEVT [MK06007]


title: pho92_7H_R2

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1

value: diploid meiotic yeast


title: WT_0h_R3

description:
50 nt read length
Table S1

value: WT


title: S8_iEVT [MK06011]

source_name: extravillous trophoblasts isolated in-situ from decidual tissue

value: decidua basalis

value: 7 - 8th week of gestation


title: S3_TB-ORG-EVT [MK06006]

value: trophoblast organoids


title: pho92_6H_R2

description:
50 nt read length
Table S1

value: pho92 mutant


title: LPS_C4

value: LPS


title: pho92_5H_R2

description:
50 nt read length
Table S1


title: pho92_3H_R2

description:
50 nt read length
Table S1


title: S5_iEVT [MK06008]


title: S2_iEVT [MK06005]


title: pho92_0h_R2

description:
50 nt read length
Table S1


title: DCVC_C2


title: Control_D1

value: Control


title: Microwell-seq datasets of Zebrafish_3m_COL33

value: AB


title: Microwell-seq datasets of Zebrafish_3m_COL30


title: Control_C1


title: S1_pEVT [MK06004]


title: ime4_7H_R2

description:
50 nt read length
Table S1

value: ime4 mutant


title: Microwell-seq datasets of Zebrafish_3m_COL35


title: Microwell-seq datasets of Zebrafish_3m_COL39


title: DCVC_LPS_C3


title: Mtm1 KO, Day35, rep4

city: Toronto

first: James

middle: J

last: Dowling

state: Ontario

address: 686 Bay Street

institute: Hospital for Sick Children

data_processing:
The sequencing reads were first aligned to the mouse genome (GRCm38) using STAR (v2.6.1) and gene uantification was done by using RSEM(v1.2.22).
Differential expression analysis were performed using DESeq2
For the purpose of this longitudinal study, samples from each time point were analyzed together.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include the RSEM expected count values for each Sample. Rows = genes; Columns = samples.

source_name: Skeletal Muscle

extract_protocol:
Total RNA was harvested using Rneasy Kit (Qiagen) and PolyA-tailed RNA was isolated from total RNA using the NEBNext poly(A) mRNA Isolation module
RNAseq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

tag: strain background

value: Skeletal Muscle

value: KO

value: Day 35


title: Microwell-seq datasets of Zebrafish_3m_COL36

extract_protocol:
Whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

value: 3 month (90 day)

value: whole organism


title: pho92_2H_R2

description:
50 nt read length
Table S1


title: ime4_6H_R2

description:
50 nt read length
Table S1


title: Microwell-seq datasets of Zebrafish_3m_COL29


title: ime4_9H_R2

description:
50 nt read length
Table S1


title: ime4_5H_R2

description:
50 nt read length
Table S1


title: LPS_B4


title: Microwell-seq datasets of Zebrafish_3m_COL34


title: DCVC_B2

value: DCVC


title: DCVC_LPS_B3


title: Mtm1 KO, Day35, rep3


title: Microwell-seq datasets of Zebrafish_3m_COL28


title: Microwell-seq datasets of Zebrafish_3m_COL25


title: ime4_2H_R2

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1


title: Microwell-seq datasets of Zebrafish_3m_COL32


title: Mtm1 KO, Day35, rep1


title: Mtm1 KO, Day21, rep4

value: Day 21


title: Control_B1


title: ime4_3H_R2

description:
50 nt read length
Table S1

value: diploid meiotic yeast


title: Microwell-seq datasets of Zebrafish_3m_COL26


title: ime4_0h_R2

description:
50 nt read length
Table S1


title: DCVC_LPS_A3


title: Mtm1 KO, Day21, rep3


title: Mtm1 KO, Day35, rep2


title: Microwell-seq datasets of Zebrafish_3m_COL15


title: Mtm1 KO, Day21, rep2


title: WT_7H_R2

description:
50 nt read length
Table S1

value: WT


title: Microwell-seq datasets of Zebrafish_3m_COL14


title: WT_9H_R2

description:
50 nt read length
Table S1


title: Mtm1 KO, Day14, rep4

value: Day 14


title: DCVC_A2


title: Microwell-seq datasets of Zebrafish_3m_COL4


title: Control_A1


title: Microwell-seq datasets of Zebrafish_3m_COL13


title: WT_5H_R2

description:
50 nt read length
Table S1


title: LPS_A4


title: WT_3H_R2

description:
50 nt read length
Table S1


title: Microwell-seq datasets of Zebrafish_3m_COL16


title: Mtm1 KO, Day14, rep3


title: Microwell-seq datasets of Zebrafish_3m_COL3


title: WT_2H_R2

description:
50 nt read length
Table S1


title: WT_2

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

description: WT

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15  with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with  coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: Arabidopsis TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields

organism: Arabidopsis thaliana

growth_protocol: Seeds were sown on peat mix in square pots in reach-in chambers at 12hrs daylenght (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany).
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the Illumina (HiSeq X-Ten) system.

treatment_protocol: 3 progenies plants from each of the 4 epi populations (epi8, epi24, epi10, epi19) and Col-0 WT were sequenced. Epi8 and epi 24 were derived from same cross while epi 10 and epi19 were from the same cross. Leaves at bolting were flash freezed in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen.

tag: replicate type

value: biological rep 2

value: rosette leaves

tag: developmental stage

value: bolting


title: Mtm1 KO, Day14, rep1


title: WT_3

description: WT

value: biological rep 3


title: WT_6H_R2

description:
50 nt read length
Table S1


title: Mtm1 KO, Day14, rep2


title: Mtm1 KO, Day21, rep1


title: pho92_9H_R1

description:
50 nt read length
Table S1

value: pho92 mutant


title: WT_0h_R2

description:
50 nt read length
Table S1


title: Mtm1 KO, Day1, rep4

value: Day 1


title: Mtm1 KO, Day1, rep3

value: Skeletal Muscle


title: WT_1

description: WT

value: biological rep 1


title: pho92_7H_R1

description:
50 nt read length
Table S1


title: epi8_3


title: pho92_6H_R1

description:
50 nt read length
Table S1


title: Mtm1 KO, Day1, rep2

value: KO


title: epi8_2


title: Mtm1 KO, Day1, rep1


title: pho92_5H_R1

description:
50 nt read length
Table S1


title: epi8_1


title: Mtm1 WT, Day35, rep4

value: Day 35


title: pho92_3H_R1

description:
50 nt read length
Table S1


title: epi24_3


title: Mtm1 WT, Day35, rep3


title: pho92_2H_R1

description:
50 nt read length
Table S1


title: epi24_2


title: lncRNA and mRNA expression data from adjacent tissue [84_adj]

type: RNA

city: Luzhou

first: Muhan

last: Lv

state: Sichuan

address: Third Section of Zhongshan Road

institute: Southwest medical university

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: ajdacent tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: ESCC tissues and matched adjacent tissues and metastasis tissues

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Tissues from ESCC surgury and promptly frozen in liquid nitrogen.

tag: subject status

value: ESCC (esophageal squamous cell carcinoma) patient

tag: gender

value: male

value: esophagus

tag: tissue type

value: ajdacent tissue


title: lncRNA and mRNA expression data from metastasis tissue [85_me]

source_name: metastasis tissue

value: metastasis tissue


title: lncRNA and mRNA expression data from cancer tissue [62_ca]

source_name: ESCC tissue

value: ESCC tissue


title: lncRNA and mRNA expression data from metastasis tissue [40_me]


title: lncRNA and mRNA expression data from adjacent tissue [63_adj]


title: lncRNA and mRNA expression data from adjacent tissue [39_adj]


title: lncRNA and mRNA expression data from metastasis tissue [64_me]


title: lncRNA and mRNA expression data from cancer tissue [83_ca]


title: Mtm1 WT, Day35, rep2

value: WT


title: DKO rep7

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

data_processing:
RNA-seq mapping and quantitation was done using STAR v. 2.6.1a with flags --runMode alignReads mThreadN 10 --genomeDir GenomeDir --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --outSAMstrandField intronMotif with --genomeDir pointing to a GRCz11/danRer11 STAR index.
The mapped reads were further analyzed by HTSeq-count v.0.11.2 and annotated using RefSeq database.
The expression levels for each transcript were quantified by FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Differential expression analysis was performed using DESeq2 v.1.32.0 on count data comparing DKO (rbfox1l-/-; rbfox2-/-) vs. sibling control (CTRL) samples.
The dedicated splicing analysis algorithm rMATS v.4.2 19 was run on the data as rmats.py with flags --readLength 150 --nthread -t paired pointing to the same GTF file and STAR index.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Heart

extract_protocol:
Embryonic hearts were lysed in TRIzol reagent (Invitrogen) and total RNA purified by RNA microPrep (Zymo Research, R2062) for each biological replicate. Purified RNA eluates were kept at -80C prior to sequencing.
RNA samples were analyzed by TapeStation (Agilent) and libraries were generated and sequenced using Ultralow Input RNA-seq (Genewiz). RNA was processed with poly(A) selection for full length transcripts. Libraries were sequenced on an Illumina HiSeq platform using the 2x150bp configuration with single index.

value: Tubingen

value: embryonic heart

value: DKO (rbfox1l-/-; rbfox2-/-)


title: Mtm1 WT, Day35, rep1


title: ime4_9h_R1

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1

value: diploid meiotic yeast

value: ime4 mutant


title: Mtm1 WT, Day21, rep3

value: Skeletal Muscle

value: Day 21


title: Mtm1 WT, Day21, rep4


title: epi19_2

value: biological rep 2

value: rosette leaves

value: bolting


title: epi19_1

value: biological rep 1


title: epi19_3

value: biological rep 3


title: DKO rep8


title: epi24_1


title: DKO rep5


title: lncRNA and mRNA expression data from cancer tissue [38_ca]

value: ESCC (esophageal squamous cell carcinoma) patient

value: male

value: esophagus


title: ime4_6h_R1

description:
50 nt read length
Table S1


title: ime4_7h_R1

description:
50 nt read length
Table S1


title: epi10_3


title: DKO rep4


title: pho92_0h_R1

description:
50 nt read length
Table S1

value: pho92 mutant


title: DKO rep3

value: Tubingen


title: Mtm1 WT, Day21, rep2

value: WT


title: ime4_5h_R1

description:
50 nt read length
Table S1


title: DKO rep6

value: embryonic heart

value: DKO (rbfox1l-/-; rbfox2-/-)


title: ime4_3h_R1

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1

value: diploid meiotic yeast


title: ime4_2h_R1

description:
50 nt read length
Table S1

value: ime4 mutant


title: Mtm1 WT, Day21, rep1

value: Skeletal Muscle

value: Day 21


title: epi10_1

value: rosette leaves


title: Mtm1 WT, Day14, rep4

value: Day 14


title: epi10_2

value: biological rep 2

value: bolting


title: DKO rep2


title: Mtm1 WT, Day14, rep3


title: Mtm1 WT, Day14, rep2


title: Control rep6

value: sibling control


title: Mtm1 WT, Day1, rep4

value: Day 1


title: WT_9h_R1

description:
50 nt read length
Table S1


title: Mtm1 WT, Day14, rep1


title: WT_7h_R1

description:
50 nt read length
Table S1


title: Control rep7


title: WT_6h_R1

description:
50 nt read length
Table S1


title: Control rep5


title: ime4_0h_R1

description:
50 nt read length
Table S1


title: WT_5h_R1

description:
50 nt read length
Table S1


title: WT_3h_R1

description:
50 nt read length
Table S1


title: Q109_C

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Embryo

extract_protocol:
Total cellular RNA was extracted from embryos using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s recommendations. After extraction, RNA concentration and quality were analyzed using a NanoDrop DP-1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and a Bioanalyzer® (Agilent, Santa Clara, CA). All samples had a 260/280 ratio > 2.0, a 28S:18S rRNA ratios >1.8, and RNA integrity number (RIN) > 8 (8.95 ± 0.4, mean ± SEM). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37ºC to remove genomic DNA according to manufacturer’s instructions. The extracted RNA was kept at -20ºC until further analyses.
The mRNA was enriched using oligo(dT) beads. The mRNA was fragmented randomly in fragmentation buffer, followed by first strand cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina, San Diego, CA) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. Double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter, Beverly, CA). In order to select cDNA fragments of 150 base pairs in length, the library fragments were purified with AMPure XP system (Beckman Coulter). The final library was obtained by PCR amplification and purification of PCR products by AMPure XP beads (Beckman Coulter, Beverly, USA).

treatment_protocol: When a 25 ± 3 mm follicle was detected, mares were randomly allocated to a urea (n=9) or control treatment (n=10). The treatment group was fed 0.4 g of feed-grade urea (Hallway Feeds, Lexington, KY) per kg of body weight, mixed with 2.4 kg of sweet feed (Poize 10% crude protein, Hallway Feeds), molasses and mixed grass hay (8.4% crude protein). The control group received identical sweet feed, molasses and hay. Daily meals were divided in two equal amounts given in the morning and afternoon using individual feeding pens. Mares had ad libitum access to water. Mares were artificially inseminated when a 35-mm follicle was determined with 500-million progressively motile sperm pooled together from two fertile stallions. Embryo collection was done at D14 and embryos were preserved in RNAlater (Thermo Fisher Scientific, Waltham, MA) at 4ºC overnight and then kept at -80ºC until RNA isolation.

value: Embryo

value: control

value: day 14


title: Mtm1 WT, Day1, rep2

value: WT


title: Mtm1 WT, Day1, rep3


title: Q112_C


title: DKO rep1

value: Tubingen

value: embryonic heart


title: Control rep8


title: Control rep3


title: Q108_C1


title: Q107_U

value: urea


title: Control rep2


title: Q108_U


title: Q106_U


title: WT_2h_R1

description:
50 nt read length
Table S1

value: SK1 pCUP-IME1

value: diploid meiotic yeast


title: WT_0h_R1

description:
50 nt read length
Table S1


title: Q108_C2


title: Mtm1 WT, Day1, rep1

value: Skeletal Muscle


title: Control rep1


title: KP_rep3

city: Tampa

first: Alex

middle: M

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

description: RiboLace Protocol

data_processing:
raw fastq files were adapter trimmed and compressed prior to pipeline submission
compressed fastq files were submitted to the RiboToolKit pipeline
RiboToolKit outputs were used for further analysis and data interpretation
Genome_build: mm10

source_name: lung adenocarcionoma organoids

growth_protocol: Organoids were grown in custom lung organoid media and plated on matrigel washed tissue culture plates for 48 hours prior to harvest

extract_protocol:
Ribosome protected RNA fragments (RPFs) were extracted according to the RiboLace Protocol
Libraries were constructed from RPFs using the Takara SMARTer small RNA Library construction Kit
successfully generated libraries were pooled prior to sequencing

treatment_protocol: cells were treated with 100 µM cycloheximide for 5 min

value: lung adenocarcionoma organoids


title: Q106_C


title: Control rep4


title: KP_rep2

description: RiboLace Protocol


title: H5_U


title: H5_C


title: GCB_WT1

data_processing:
Raw fastq data is trimmed by trimmomatic and get Clean fastq data
Clean fastq data is mapped by Star and get Bam data
Bam data is counted by Htseqcount and get count file
Differential expression calculate use DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: counts file of each sample

source_name: GCB

extract_protocol:
Germinal center B cells were filtered using FACS.Activated B cells were get first enriched B cells from spleen using PanB biotin and SA beads, then activated B cells . RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

value: spleen

value: Germinal center B cells


title: GCB_WT2


title: KP_rep1

description: RiboLace Protocol


title: Micorwell-seq datasets of Earthworm_6m_COL4

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. For 6m earthworm dataset in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp). For 8m earthworm dataset in each COL, cellbarcode: in read1, the bases 1-6, 7-12, 13-18 are merged (18bp); UMI: in read1, the bases 19-24 (6bp).
scRNA-seq reads were aligned to the Eisenia andrei GWHACBE00000000 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Eisenia andrei GWHACBE00000000
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

organism: Eisenia andrei

value: 6 month

value: whole organism


title: Micorwell-seq datasets of Earthworm_6m_COL3


title: GCB_KO2

last: Jing

address: 101 Longmian Ave Jiangning District

institute: Nanjing Medical University

value: Jmjd1c B KO


title: AT2_rep2

description: RiboLace Protocol

source_name: alveolar type 2 organoids

value: alveolar type 2 organoids


title: F58_C

value: Embryo


title: F17_U


title: GCB_KO1


title: Micorwell-seq datasets of Earthworm_6m_COL1


title: NO-treated embryos of 21-day aged seeds rep3

status: Public on Jul 07 2022

city: Warsaw

first: Katarzyna

last: Ciacka

address: Nowoursynowska 166

country: Poland

institute: Warsaw University of Life Sciences

description:
Test 21d
NO 21d rep3
apple (Malus domestica Borkh.)

data_processing:
Expression of selected genes was determined using the method described by Vandesompele et al. (2002) and Hellemans et al. (2007). The calculations were made based on the Cq value for individual genes and the primer efficiency value. Gene expression was normalized using the two reference genes - Sar and Pdi.
Based on technical repetitions, the mean value of Cq  was calculated for each biological sample (control, treated with NO). For control (calibrator), the mean Cq value from triplicate biological replicates was calculated to create a ‘Control average Cq’. Then, the ∆Cq for each sample was calculated by subtracting the mean Cq values of the control, treated samples from the ‘Control average Ct’.  The converted primer efficiency (E) was determined using the formula:  Converted primer efficiency (E) = ((primer efficiency (%)) / 100) +1  To calculate the relative quantity (RQ) value for each sample,  E vaule was raised to the power of ΔCq.  Based on the RQ values of both reference genes, the geometric mean for the individual samples (control and treated) was calculated (Geomean[RQrefs]), and used to normalize the expression of the test genes. The gene expression was obtained by dividing the RQ value of each biological sample for the test gene by the Geomean[RQrefs] value of both reference genes of the corresponding sample.
Matrix normalized worksheet reports normalized signal (with converted primer efficiency and geomean[RQrefs] value calculated based on RQ for housekeeping genes). The controls were used as a calibrators when calculating the ∆Ct values for tested samples.
Fold change worksheet reports treated/control  (NO treated aged 7 d/aged 7d; NO treated aged 14 d/aged 14d; NO treated aged 21d/aged 21d) and progresive aged/aged for 7 d (aged 14d/ aged 7d; aged 21d/aged 7d) ratios

label: Sybr Green

organism: Malus domestica

source_name: axes of NO-treated embryos of seeds aged for 21 days

label_protocol: After treatment with DNAse I, total RNA (200 ng) was used for cDNA synthesis. cDNA was obtained using RevertAid First Strand cDNA Synthesis Kit. The finished product was diluted 3.5 times. RT-qPCR was carried out in a Bio-Rad CFX Connect™ Real-Time PCR Detection System. iTaq™ universal SYBR® Green supermix was used for the reaction. RT-qPCR were performed  with 40 cycles at 95 °C for 15 seconds and 60 °C for 30 seconds.

growth_protocol: Dry apple seeds were placed in a Petri dish filled with sterile quartz sand moistured with  sterile, distilled water. Accelerated aging was performed at 33 °C  for 7, 14, and 21 days. After aging, seeds were removed from the sand, rinsed with water, and the embryos were isolated. Part of the embryos were treated with NO. The non-treated embryos (the control, embryos isolated from seeds only subjected to accelerated aging) and the embryos isolated from seeds subjected to aging and shortly treated with NO (NO treatment) were placed in glass Petri dishes on filter paper moistened with distilled water for 48 h in a growth chamber in a 25/20 °C day/night, 12/12 h photoperiod, the light intensity of 100 µmol PAR m-2 s-1. After 48 h of the culture, the embryonic axes were isolated and used for experiments.

extract_protocol: Total RNA was isolated using RNAzol®RT (according to the Manufacturer’s instructions), followed by DNAse I treatment.

treatment_protocol: The embryos, treated with NO, were shortly fumigated with vapors of a solution of acidified nitrite (14.5 mM NaNO2, 0.2 M HCl) for 3 h. After NO fumigation, the embryos were rinsed in distilled water and cultured.

tag: plant organ

value: seeds

tag: seed treatment

value: subjected to accelerated aging for 21 days

tag: embryo treatment

value: treated with NO

tag: plant material used in analysis

value: embryonic axes


title: embryos of 21-day aged seed rep3

description:
Control 21d
Control 21d rep3
apple (Malus domestica Borkh.)

source_name: axes of embryos of seeds aged for 21 days

value: non-treated


title: embryos of 21-day aged seed rep2

description:
Control 21d
Control 21d rep2
apple (Malus domestica Borkh.)


title: NO-treated embryos of 14-day aged seeds rep2

description:
Test 14d
NO 14d rep2
apple (Malus domestica Borkh.)

source_name: axes of NO-treated embryos of seeds aged for 14 days

value: subjected to accelerated aging for 14 days


title: NO-treated embryos of 14-day aged seeds rep3

description:
Test 14d
NO 14d rep3
apple (Malus domestica Borkh.)


title: NO-treated embryos of 7-day aged seeds rep3

description:
Test 7d
NO 7d rep3
apple (Malus domestica Borkh.)

source_name: axes of NO-treated embryos of seeds aged for 7 days

value: subjected to accelerated aging for 7 days


title: NO-treated embryos of 21-day aged seeds rep2

description:
Test 21d
NO 21d rep2
apple (Malus domestica Borkh.)


title: AT2_rep1

description: RiboLace Protocol


title: NO-treated embryos of 7-day aged seeds rep2

description:
Test 7d
NO 7d rep2
apple (Malus domestica Borkh.)


title: embryos of 7-day-aged seed rep3

description:
Control 7d
Control 7d rep3
apple (Malus domestica Borkh.)

source_name: axes of embryos of seeds aged for 7 days


title: embryos of 14-day aged seed rep2

description:
Control 14 d
Control 14d rep2
apple (Malus domestica Borkh.)

source_name: axes of  embryos of seeds aged for 14 days


title: embryos of 14-day aged seed rep3

description:
Control 14 d
Control 14d rep3
apple (Malus domestica Borkh.)


title: NO-treated embryos of 21-day aged seeds rep1

description:
Test 21d
NO 21d rep1
apple (Malus domestica Borkh.)


title: embryos of 14-day aged seed rep1

description:
Control 14 d
Control 14d rep1
apple (Malus domestica Borkh.)


title: embryos of 7-day-aged seed rep2

description:
Control 7d
Control 7d rep2
apple (Malus domestica Borkh.)


title: Micorwell-seq datasets of Earthworm_6m_COL2


title: NO-treated embryos of 14-day aged seeds rep1

description:
Test 14d
NO 14d rep1
apple (Malus domestica Borkh.)


title: NO-treated embryos of 7-day aged seeds rep1

description:
Test 7d
NO 7d rep1
apple (Malus domestica Borkh.)


title: embryos of 7-day-aged seed rep1

description:
Control 7d
Control 7d rep1
apple (Malus domestica Borkh.)


title: embryos of 21-day aged seed rep1

description:
Control 21d
Control 21d rep1
apple (Malus domestica Borkh.)


title: Glycine max hypocotyl tissue - CGMPH_Psojae_rep1

city: Corvallis

first: Emily

last: Helliwell

state: OR

address: Oregon State University

institute: Oregon State University

data_processing:
Base-calling was done using RTA (Real-Time Analysis) software, and bcl files were converted to fastq using bcl2fastq
Sequenced reads were trimmed for adaptor sequence using cutadapt2 parameters -b 20 -n 2  and mapped to Glycine max v1.1 using bowtie2 with parameters -c 'tophat --num-threads 8 -P 8 -q
Count tables to quantify the number of reads per gene were generated with the samtools function htseq-count (Li et al., 2009), parameter -f
Normalization of the number of counts was run using EstimateSizeDisperson function with the R package DESeq
Assembly: Wm82.a1.v1.1 (Glyma 1.1), Gmax_189_gene.gff3
Supplementary files format and content: csv file soybean_ncounts include normalized values for each Sample ...
Supplementary files format and content: Matrix table raw_counts with raw gene counts for every gene and every sample

organism: Glycine max

growth_protocol: Six soybean seeds were sown in potting soil in 6-inch pots and maintained in growth chambers at 28˚C light/24˚C dark.

extract_protocol:
Hypocotyl segments, 1 cm long, centered on the inoculated areas were harvested 12 hr later, pooling 18 plants each for mock- and P. sojae-inoculated lines, then snap-frozen in liquid nitrogen and stored in -80˚C.  RNA was extracted using RNeasy (Qiagen) RNA extraction reagent according to the manufacturer’s instructions.
1 µg of total RNA was submitted for sequenceding on an Illumina HiSeq 3000, using a 150 base pair, paired-end module at the Oregon State University Center for Genome Research and Biocomputing

treatment_protocol: Hypocotyls on 10 day-old soybeans were wounded by gently scraping 0.5 cm between the soil line and the cotyledons, and a 2.5 mm2 square of P. sojae mycelia was placed, mycelial side down over the wounded area.  Inoculated plants were maintained in a growth chamber at 28˚C light/24˚C dark for twelve hours

tag: cell type

value: plant cells, hypocotyl tissue

value: PI-binding GMPH line C

value: Inoculated with mycelium of Phytophthora sojae Race 2


title: Area D

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description: Biological replicates 4 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

organism: Sus scrofa

source_name: Blastocyst from oocyte in control

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).

value: Blastocyst

value: control

source_name: Blastocyst from oocyte exposed to high NEFAs

value: oocyte exposed to high NEFAs


title: Area A

description: Biological replicates 1 of 4


title: Glycine max hypocotyl tissue - CGMPH_Psojae_rep2

tag: strain


title: Glycine max hypocotyl tissue - CGMPH_Psojae_rep3


title: Area C

description: Biological replicates 3 of 4


title: Glycine max hypocotyl tissue - BGMPH_Psojae_rep3

value: PI-binding GMPH line B


title: Area B

description: Biological replicates 2 of 4


title: Glycine max hypocotyl tissue - BGMPH_Psojae_rep2


title: Glycine max hypocotyl tissue - VAM13_Psojae_rep3

value: PI-binding VAM line 13


title: Glycine max hypocotyl tissue - VAM19_Psojae_rep3

value: PI-binding VAM line 19


title: Glycine max hypocotyl tissue - VAM19_Psojae_rep2


title: Glycine max hypocotyl tissue - VAM19_Psojae_rep1


title: Glycine max hypocotyl tissue - VAM13_Psojae_rep1


title: Glycine max hypocotyl tissue - Vmut_Psojae_rep2

value: non-binding VAM mutant


title: Area B

type: genomic

description: Biological replicates 2 of 4

hyb_protocol: Hybridizations were performed according to the microarray manufacturer’s instructions (Agilent Technologies). Briefly, 500 ng of labeled sample (in 22 μL) was mixed with 61 μL of hybridization master mix containing 5 μL of Cot-1 (1 mg/ml) , Applied Genetics Laboratories), 1μL of Agilent 100x Blocking Agent and 55 μL of Agilent 2× HI-RPM Hybridization Buffer (Agilent Technologies). Samples were held at 95°C for 3 min and at 37°C for 30 min followed by addition of 27 μL of Agilent-CGHBlock (final volume 110 μL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab) for 40 h at 65°C and 20 rpm. Washing was carried out according to the microarray manufacturer’s instructions

scan_protocol: Scan on a PowerScanner (Tecan) at 2um using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: The array data analysis methods and downstream analysis pipelines are described in detail in (Saadi et al., 2014). Briefly, after Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and thus, Bayesian statistics of differential expression were obtained. Thus, differentially methylated probes were identified using linear models for microarray data (LIMMA).

label_protocol: For each sample, 1 μg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology) according to the manufacturer’s instructions with minor modifications: 1 μL of Cy-ULS dye was added per 1 μg of genomic DNA adjusted with 10× labeling buffer. The labelling mixture was then held for 30 min at 85°C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 25 μL 1/10 Buffer EB. A 1.5 μL aliquot was used to determine DNA concentration and dye incorporation using the ND- 1000 NanoDrop.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
The methodology have been thoroughly describef in (Saadi et al., 2014). Briefly, 10ng of DNA sample and spike-in control were cut in ≈160bp fragment using MSEI restriction enzyme. MseLig 12 and MseLig 21 adapters were added to the fragmented gDNA sites. Sample were the digested using methyl sensitive restriction enzyme HpaII, HinP1I and AciI. Only unmethylated fragment have been targeted by those enzyme, leaving only one adapter on the cleaved fragment. Efficiency of the digestion was confirmed by analyzing the spike-in control added prior to the DNA fragmentation step. For the step, qPCR was performed by preparing a separate mixes containing forward and reverse primer targeting HpaII, HinP1I and AciI site. Undigested spike-in (1/1000 dilution) was used as a positive control and non-template controls were also added as negatives control. The amplification plot and the dissociation curve were evaluated for each primer set separately. The DNA fragmentation was considered successful when the threshold cycle (ct) was greater than 5 when compared to the undigested control.Fragment selection by ligation-mediated PCR After cleavage by methyl sensitive enzyme, the gDNA was purified by ethanol precipitation and dissolve in nuclease free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR). The PCR products were resolved on 0.8% agarose gel to assess the quality. Then the previously added linker were removed.


title: Area A

description: Biological replicates 1 of 4


title: Area D

description: Biological replicates 4 of 4


title: Area C

description: Biological replicates 3 of 4


title: Glycine max hypocotyl tissue - Vmut_Psojae_rep1


title: Glycine max hypocotyl tissue - Vmut_Psojae_rep3


title: Glycine max hypocotyl tissue - null_Psojae_rep3

value: null segregant


title: Glycine max hypocotyl tissue - CGMPH_mock_rep3

value: Inoculated with sterile water


title: Glycine max hypocotyl tissue - CGMPH_mock_rep1


title: Glycine max hypocotyl tissue - null_Psojae_rep2


title: Glycine max hypocotyl tissue - VAM19_mock_rep1


title: Glycine max hypocotyl tissue - CGMPH_mock_rep2


title: Glycine max hypocotyl tissue - BGMPH_mock_rep2


title: Glycine max hypocotyl tissue - BGMPH_mock_rep1


title: Glycine max hypocotyl tissue - BGMPH_Psojae_rep1


title: Glycine max hypocotyl tissue - VAM13_Psojae_rep2


title: Glycine max hypocotyl tissue - VAM13_mock_rep3


title: Glycine max hypocotyl tissue - VAM19_mock_rep2


title: Glycine max hypocotyl tissue - VAM13_mock_rep1


title: Glycine max hypocotyl tissue - null_Psojae_rep1


title: Glycine max hypocotyl tissue - Vmut_mock_rep3


title: Glycine max hypocotyl tissue - null_mock_rep3


title: Glycine max hypocotyl tissue - Vmut_mock_rep2


title: Glycine max hypocotyl tissue - BGMPH_mock_rep3


title: Glycine max hypocotyl tissue - VAM19_mock_rep3


title: Glycine max hypocotyl tissue - null_mock_rep1


title: Glycine max hypocotyl tissue - Vmut_mock_rep1


title: CK_CTRL_2

city: Tokyo

first: Iki

last: Sonn

address: Shinjyuku-ku, Shinanomachi 35

country: Japan

institute: Keio University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 genome using HISAT2.
Sequence counts were calculated by Featurecounts.
Genome_build: Hg38
Supplementary_files_format_and_content: Raw counts

growth_protocol: Feeder-free SPI1 plasmid transfected iPSCs were cultured according to protocol published by CiRA. Then cells were transferred into StemPro™-34 SFM  medium and supplied with multiple cytokines according to different stages of differentiation (more details in the text). On Day 16, floating cells were collected and re-plated into PDL-coated plate, cultured in DMEM/F12 medium supplied by IL-34, TGFβ1, MCSF, CD200L and CX3CL1. Half medium change were applied every two days.

extract_protocol:
Cells were collected by RLT buffer and then homogenized by QIAshredder (Qiagen #79656). Total RNAs were isolated by RNeasy Mini Kit (Qiagen #74106) following manufacture’s guideline
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10ng/ml Dox were added into medium from Day 6.

value: iPSCs-derived microglia

tag: iPS strain

value: Cytokine alone


title: HEK293-SEQ2

city: Yanghzou

first: Songlei

last: Xue

address: Wenhui Road 48#

institute: Yangzhou University

description:
HEK293-SEQ2
293TK2

data_processing:
Bcl2fastq (v2.17.1.14) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence withCutadapt（version 1.9.1）. then mapped to HG19 whole genome usingHisat2(v2.0.1).
Gene Expression: HTSEQ v0.6.1, assembly: Stringtie V1..0.4
Different expression gene analysis: DESeq2 V1.6.3, DESeq v1.18.0, EdgeR V3.4.6
Genome_build: hg19
Supplementary_files_format_and_content: excel format: Count and  Reads Per Kilo bases per Million reads

source_name: HEK293 Cell

extract_protocol:
RNA was harvested using Trizol reagent.NEBNext® rRNA Depletion Kit (New England Biolabs, USA) removed ribosomal RNA (rRNA) from 2 μg of total RNA. The purified rRNA-removed RNA was treated using the EZ RNA methylation Kit (Zymo Research). Then the TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) was used to construct the sequencing library.t was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: comparation of HEK293-TRDMT1-KD and  HEK293 control

tag: genotype

value: Control


title: PU_2

tag: treatment

value: PU.1 over-expresssion by Tet-on


title: HEK293-SEQ3

description:
HEK293-SEQ3
293TK3


title: PU_1


title: HEK293-TKD3

description:
HEK293-TKD3
293C3

value: TRDMT1 gene knockdown


title: HEK293-TKD2

description:
HEK293-TKD2
293C2


title: Glycine max hypocotyl tissue - VAM13_mock_rep2

value: plant cells, hypocotyl tissue


title: HEK293-SEQ1

description:
HEK293-SEQ1
293TK1


title: HEK293-TKD1

description:
HEK293-TKD1
293C1


title: Perturb-seq Ultima

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: 3' Perturb-seq data, sequenced with Ultima

data_processing:
cellranger mkfastq v5.0 was used to generate fastq files for Illumina data
For Ultima and Single End Illumina data, Cutadapt v2.10 was used to remove adapters and qualitfy filter. For 3' data reads without 8 T's from the poly(T) region were discarded. Cutadapt and SeqKit v0.15.0 were used to split these read into 2 pieces for later processing. We removed reads whose cDNA sequence was < 50bp.
seqtk v1.0 was used to downsample the Ultima data to the appropriate level
CellRanger count v5.0 was used to quanifty the number of UMIs per cell in each sample, with CellRanger vdj being used for TCR and BCR data.
CellSNP-lite v1.2.0  and Vireo v0.5.5 were used to identify genotype clusters in the 5' mixture data
Demux-EM v0.1.7  was used to assign cells to hash tag IDs in the Perturb-seq data
Seurat v4.0.0 was used for clustering and downstream analysis
Assembly: hg38
Supplementary files format and content: Most processed data are in MM format, with 3 files per sample: the cell names file, the gene names file, and the MM file with gene by cell UMI count matrix. In addition have h5 files from CellRanger for the Perturb-seq results, including UMI counts from the HTO, ADT, and Guide data. The csv files are for TCR and BCR data produeced by CellRanger vdj.

source_name: A375 cell line

growth_protocol: Perturb-seq only: Perturbed cells selection with puromycin, details see manuscript

extract_protocol: 10x Chromium Next GEM single cell 3' (v3.1) and 5' (v2) gene expression assays

treatment_protocol: Perturb-seq only: Selected perturb-seq cells treated with recombinant IFNγ, details see manuscript

tag: 10x technology

tag: sample type

value: Cell Line