title: D002 colonised poplar root 3

description:
Library name: D002_ECM_3
This sample ist from P.microcarpus strain D002 colonised poplar roots. It is the third of three biological replicates used in this experiment.

value: colonised poplar root


title: RNA_D7_Rosa_805

status: Public on Jul 01 2025

type: SRA

city: Beijing

first: Jing

last: Han

address: qinghuayuan

country: China

institute: Tsinghua university

library_source: transcriptomic

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10
Supplementary files format and content: raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: pancreas

extract_protocol:
300 GFP-positive cells and 10,000 GFP-positive cells were sorted by FACS for small scale RNA-seq and ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A). Small scale RNA-seq library was constructed using Smart-seq2 method with modifications allowing higher quality library generation from pancreatic cells. Briefly, mouse pancreatic cells were directly sorted into 8 μl of denaturing lysis buffer (6 M guanidine HCl, 0.2% (vol/vol) Triton X-100 and 1% (vol/vol) β-mercaptoethanol). RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2X) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.
Smart-seq2 protocol.

tag: tissue

value: pancreas

tag: cell line

tag: cell type

value: pancreatitis

tag: genotype

value: control

tag: treatment


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 022

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_022
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

molecule: nuclear RNA

organism: Sorghum bicolor

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

value: seedling

tag: age


title: OE1

city: Guanzghou

first: Zihang

last: Yu

state: Please Select

address: GuangZhou Avenue

institute: Southern Medicla University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts and TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
Then the enriched mRNAwasfragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: cancer cell

value: DCBLD2 overexpression


title: D002 colonised poplar root 2

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
Library name: D002_ECM_2
This sample ist from P.microcarpus strain D002 colonised poplar roots. It is the second of three biological replicates used in this experiment.

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files.
raw reads were paired, trimmed (quality limit=0.05, automatic read through adapter trimming, discard short reads) and mapped against Pisolithus microcarpus 441  v2 primary scaffolds transcripts (https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html) using CLC Genomics Workbench v23.0.5 (Qiagen, Courtaboeuf, France).
For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.8, and the maximum number of hits for a read was set to 10.
Differentially expressed genes (DEGs) were calculated using DESeq2 (v1.32) and unique mapped gene reads as entry .
Condition-specific differentially expressed genes (DEGs) were identified for each pairwise condition, using a false discovery rate (FDR) < 0.05 and a log2 fold-change (Log2FC) ≥ |1| as cut-off.
Assembly: https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html
Supplementary files format and content: tab-delimited text files include Protein ID, raw counts, RPKM, TPM and CPM values for each sample

organism: Pisolithus microcarpus

source_name: colonised poplar root

growth_protocol: In vitro interactions were established between the hybrid poplar clone and parental dikaryon and sibling monokaryons of P. microcarpus. The MMN medium used had low phosphorus and nitrogen content and was lined with cellophane membranes. Ten to twelve agar discs containing fungal mycelia were placed on cellophane membranes and kept at 25°C for 20 days. Two poplar plants were transferred to the fungal mycelium. Petri dishes were incubated in a growth chamber at 25°C with 16 h of light per day for 30 days. Fungal controls (free-living mycelium, FLM) were included in the experiment. Minimum three replicates were performed for each isolate.

extract_protocol:
Total RNAs was extracted from ECM tissues and FLM of the parental dikaryon (D002) and three selected monokaryons (M057, M091, and M120) using a CTAB and lithium chloride-based method (Chang et al., 1993). We selected these monokaryon strains based on their ability to form ECMs with poplar clones. Total RNA was quantified, and integrity waschecked using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA).
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 125 bp Illumina HiSeq2500 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

tag: strain


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 021

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_021
sci-RNA-seq3
L1_rice_combined.RData


title: RNA_D7_Rosa_724


title: C3

value: WT


title: D002 colonised poplar root 1

description:
Library name: D002_ECM_1
This sample ist from P.microcarpus strain D002 colonised poplar roots. It is the first of three biological replicates used in this experiment.


title: ATAC_PDAC_cell_3_control_9270

library_source: genomic

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
10,000 GFP-positive cells were sorted by FACS for ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).
ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).

value: tumor

value: no


title: C2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 020

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_020
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 026

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_026
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_PDAC_cell_3_Chd4_4


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 019

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_019
sci-RNA-seq3
L1_rice_combined.RData


title: OE3


title: ATAC_PDAC_cell_3_control_4841


title: RNA_tumor_Rosa_953

value: PDAC


title: D002 free-living mycelium 1

description:
Library name: D002_FLM_1
This sample ist from P.microcarpus strain D002 free-living mycelium. It is the first of three biological replicates used in this experiment.

source_name: free-living mycelium

value: free-living mycelium


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 017

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_017
sci-RNA-seq3
L1_rice_combined.RData


title: D002 free-living mycelium 3

description:
Library name: D002_FLM_3
This sample ist from P.microcarpus strain D002 free-living mycelium. It is the third of three biological replicates used in this experiment.


title: C1


title: D002 free-living mycelium 2

description:
Library name: D002_FLM_2
This sample ist from P.microcarpus strain D002 free-living mycelium. It is the second of three biological replicates used in this experiment.


title: AAI3

city: Guangzhou

first: Ziqi

last: Liu

state: Guangdong Province

address: 2nd Zhongshan Road

institute: Sun Yat-sen University

description: Expression profiling by high throughput sequencing

data_processing:
For each biorep of screening experimental or control condition, add a pseudocount of 1 to the NGS read count of each sgRNA and normalize by the total number of NGS read counts for that condition. To obtain the sgRNA fold change, divide the experimental normalized sgRNA count by the control and take the base 2 logarithm.
Prepare a RIGER input .csv file with the column headers ‘WELL_ID’, ‘GENE_ID’, and ‘biorep 1’, ‘biorep 2’, etc from left to right. ‘WELL_ID’ is a list of sgRNA identification numbers, ‘GENE_ID’ is a list of the genes that the sgRNAs target, and the ‘biorep’ columns show the sgRNA fold change. Each row contains a different sgRNA in the library.
RIGER is launched through GENE-E from the Broad Institute (http://www.broadinstitute.org/cancer/software/GENE-E/download.html). Start GENE-E and import the input .csv file by navigating to File > Import > Ranked Lists. Click the table cell containing the first data row and column as instructed. Launch RIGER by going to Tools > RIGER.
Once the RIGER analysis has completed, export the gene rank data set. Determine the top candidate genes based on either the overlap or the average ranking between the screening bioreps.
Assembly: None
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: PCR-NGS

source_name: Cell line

extract_protocol:
At the end of the screen, harvest genomic DNA (gDNA) from a sufficient number of cells to maintain a coverage of >500 using the Zymo Research Quick-gDNA MidiPrep according to the manufacturer’s protocol. Elution was performed twice with 150 μl each for maximum recovery of gDNA. Amplify the sgRNA for NGS. Scale up the number of reaction such that all the gDNA harvested from the screen is amplified. Each 50-μl reaction can hold 1 μg of gDNA. Using a illlumina NovaSeq6000 to perform the NGS for sgRNAs.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Cell line

value: Renal proximal tubular cell

value: Wild type

value: AAI (IC 80)


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 016

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_016
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 018

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_018
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_PDAC_cell_3_Chd4_2


title: AAI2


title: total_RNAseq_Djasinga_orangutan_iPSC_biol_rep_3

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbruck Center for Medicine

description:
Library name: sample2_rep3
rRNA_depleted

data_processing:
Total RNAseq data were aligned to ponAbe3 genome by STAR with following options: ‘--alignIntronMin 15 --outSAMstrandField intronMotif  --outFilterMultimapNmax 50 --twopassMode Basic’. Transcript prediction with Stringtie with options ‘-s 20 -f 0.2 -m 50 ‘ followed by merging all identified HERVHLin -overlapping transcripts with ‘stringtie –merge’  was used to create single transcript annotation. Reconstructed transcripts were compared to the reference annotations with gffcompare with options ‘-T -C -R -r <reference.gtf> -s <ref_genome.fa> <per-species.predicted.gtf>’.
Raw sequencing reads were assessed for quality using FastQC (v0.11.9). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39) with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The resulting high-quality reads were used for subsequent analysis.
Assembly: ponAbe3
Supplementary files format and content: orang_TPMs.xlsx

organism: Pongo abelii

growth_protocol: cells were cultured on StemMACS™ iPS-Brew media, 1uM IWR1, 0.5uM CHIR, matrigel coating, passaged in clumps with versene for 3 sequential passages

extract_protocol:
Direct-zol RNA Miniprep (Zymo Research), in column DNAse treatment
DNBseq (UMI) small RNAseq BGI, Illumina Stranded Total RNA protocol

value: induced pluripotent stem cells

value: total small RNA

value: differentiated IPSc

tag: batch

value: replicate 3


title: ATAC_PDAC_cell_2_Smarca4_6

value: pancreas


title: ATAC_PDAC_cell_2_control_4841

value: control


title: deltaFis_MicroC_biol_rep2

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description: Library name: ag62

data_processing:
The raw reads were processed with distiller-nf pipeline using NC_000913.3 E.coli reference genome and BWA as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: cooler (.cool, a contact matrix) file for each sample

organism: Escherichia coli

source_name: bacteria

growth_protocol: E. coli K-12 MG1655 strain was grown in Luria-Bertani broth at 37 °C and 200 rpm until reaching an OD600 of ~ 0.6.

extract_protocol: Cells were fixed with 3% formaldehyde and 2 mM DSG followed by treatment with lysozyme. DNA was digested with MNase. DNA ends were labeled with biotin and ligated followed by removal of biotin from non-ligated ends by Exonuclease III. The sample was de-crosslinked at 65 °C in the presence of Proteinase K followed by phenol-chloroform extraction and ethanol precipitation. RNA was removed by RNase A treatment and DNA was further purified with AMpure XP beads. Downstream steps included sonication, biotin pull down, end repair, A-tailing, ligation of Illumina Y adapters, and PCR amplification.

treatment_protocol: For heat shock treatment, cells were incubated in a water bath at 44 °C for 10 min. For transcription inhibition, cells were treated with 25 or 750 µg/mL rifampicin for 40 min at 37 °C and 200 rpm. To induce DNA damage, cells were exposed to 70 µg/mL bleomycin for 10 min at 37 °C and 200 rpm. For DNA gyrase inhibition, cells were treated with 0.025 or 0.25 µg/mL ciprofloxacin or 25 or 250 µg/mL novobiocin for 15 min at 37 °C and 200 rpm. For netropsin treatment, cells were grown to an OD600 ~ 0.4, followed by the addition of netropsin to a final concentration of 20 or 200 µg/mL and incubation for 30 min at 37 °C and 200 rpm.

value: bacteria

value: delta Fis


title: ATAC_PDAC_cell_1_Srcap_4

value: SrcapKO


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 012

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_012
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: AAI1


title: ATAC_PDAC_cell_2_Smarca4_4

value: tumor

value: no


title: Con3

value: Control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 015

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_015
sci-RNA-seq3
L1_rice_combined.RData


title: total_RNAseq_Dokana_orangutan_iPSC_biol_rep_3

description:
Library name: sample1_rep3
rRNA_depleted

treatment_protocol: Direct-zol RNA Miniprep (Zymo Research), in column DNAse treatment


title: ATAC_PDAC_cell_2_control_9270


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 014

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_014
sci-RNA-seq3
L1_rice_combined.RData


title: deltaFis_MicroC_biol_rep1

description: Library name: ag61


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 010

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_010
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 4, 0 hours, Kit B

city: Seoul

first: Jae Won

last: Yun

address: 53, Jinhwangdo-ro 61-gil, Gangdong-gu

department: VHS Research Institute

country: South Korea

institute: Veterans Health Service Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic program.
Trimmed sequence reads were mapped using HISAT2 program.
Aligned reads were assembled using StringTie program.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Whole blood

extract_protocol:
RNA was harvested using QIAamp RNA blood mini kit (Qiagen) and High Pure RNA isolation kit (Roche). Total RNA > 0.7 ug was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Globin Kit following manufacturer's protocols.

value: Whole blood

value: 4 C refrigeration, RNA extraction kit B


title: Con2

value: Cell line

value: Renal proximal tubular cell

value: Wild type


title: Con1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 013

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_013
sci-RNA-seq3
L1_rice_combined.RData


title: total_RNAseq_Djasinga_orangutan_iPSC_biol_rep_2

description:
Library name: sample2_rep2
rRNA_depleted

value: induced pluripotent stem cells

value: total small RNA

value: replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 009

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_009
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 4, 24 hours, Kit B


title: total_RNAseq_Djasinga_orangutan_iPSC_biol_rep_1

description:
Library name: sample2_rep1
rRNA_depleted

value: differentiated IPSc

value: replicate 1


title: Subject 3, 48 hours, Kit B


title: ATAC_PDAC_cell_1_Srcap_1

value: pancreas


title: Subject 4, 24 hours, Kit A

value: 4 C refrigeration, RNA extraction kit A


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 011

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_011
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_PDAC_cell_1_Smarca5_3


title: total_RNAseq_Dokana_orangutan_iPSC_biol_rep_2

description:
Library name: sample1_rep2
rRNA_depleted


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 008

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_008
sci-RNA-seq3
L1_rice_combined.RData


title: pbap2-tr-DiCre_Rapa-

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

description: Library name: Sample1

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: txt, raw read count

organism: Plasmodium berghei ANKA

source_name: ANKA

growth_protocol: pbap2-tr-DiCre was subjected to cultures and split into two. To one culture, 3/20 volume of rapamycin (Wako) solution (200 μM DMSO stock) was added final concentration of 30 nM. To the other, the same volume of DMSO was added as a control. These parasites were cultured for 16 h, and the schizonts were harvested and injected into mice. Parasites were then harvested for RNA extraction at 12 hpi.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s instructions.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems),

treatment_protocol: In cultures, parasites were treated with 30 nM rapamycin (Rapa+) or DMSO (Rapa-).

value: ANKA

value: trophozoite

value: DMSO


title: ATAC_PDAC_cell_1_Smarca5_2

value: tumor

value: no


title: total_RNAseq_Dokana_orangutan_iPSC_biol_rep_1

description:
Library name: sample1_rep1
rRNA_depleted


title: ATAC_KCa_tumor_Smarca5_899


title: ATAC_PDAC_cell_1_control_9270_2

value: control


title: pbap2-tr-DiCre_Rapa+

description: Library name: Sample2

value: rapamycin


title: ATAC_PDAC_cell_1_control_9270_1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 007

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_007
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: Subject 3, 48 hours, Kit A

value: Whole blood


title: Subject 3, 0 hours, Kit B

value: 4 C refrigeration, RNA extraction kit B


title: Subject 3, 0 hours, Kit A


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 005

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_005
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 006

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_006
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_tumor_Smarca5_876


title: PbMORC_ChIP_1

description: Library name: Sample3

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm with the --call-summits option.
Assembly: PlasmoDB, version 3
Supplementary files format and content: text, Peak-calling

growth_protocol: PbAP2-TR::GFPpbap2-g(-) and PbMORC::GFPpbap2-g(-) parasites were each  cultured for 16 h, and mature schizonts formed in the cultures were harvested by density gradient centrifugation using Iodixanol solution (Optiprep) and were then injected into mice. The parasites were harvested for ChIP experiments at 12 hours post-injection (hpi).

extract_protocol:
Infected blood was filtered with Plasmodipur to remove lymphocytes. The samples were then fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 1.5 M NH4Cl, residual cells were lysed in SDS lysis buffer. The lysates were sonicated with Bioruptor in the following condition: 30/30 s interbals for 20 times with middle power. After centrifugation of the sonicated lysates, the supernatants were subjected to immunoprecipitation with anti-GFP antibodies conjugated on Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),

value: Trophozoite


title: Subject 4, 0 hours, Kit A


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 004

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_004
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_tumor_Rosa_874


title: PbAP2-TR_ChIP_2

description: Library name: Sample2


title: PbAP2-TR_ChIP_1

description: Library name: Sample1


title: Subject 2, 24 hours, Kit B


title: ATAC_KCa_tumor_Rosa_870


title: PbMORC_ChIP_2

description: Library name: Sample4


title: ATAC_KCa_tumor_Rosa_827


title: Subject 1, 16 days, Kit A


title: ATAC_KCa_tumor_Rosa_865


title: pbap2-g_KO_16h

description: Library name: Sample3

growth_protocol: pbap2-g(-) was cultured for 16 h, and mature schizonts formed in the cultures were harvested by density gradient centrifugation using Iodixanol solution (Optiprep) and were intravenously injected into mice.  Parasites were then harvested for RNA extraction at 4, 8, 16 h post-injection.

value: pbap2-g KO


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 192

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_192
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 003

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_003
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 001

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_001
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 2, 0 hours, Kit B


title: ATAC_KCa_tumor_Smarca5_872


title: COS70FB3

city: Daejeon Metropolitan City

first: SHIN

last: NARI

address: Oncheon 2-dong, Yuseong-gu

institute: chungnam national university

data_processing:
High quality clean data was used for all the downstream analyses after removing reads containing adapter, ploy-N and low-quality from the raw data. Raw reads from each sample were processed by trimming adaptor sequences and discarding the reads with unknown nucleotides > 5%, long oligo Ts > 50, as well as low-quality reads (Phred scores Q < 20) using Trimmomatic (v. 0.32).
Assembly: Tcas5.2
Supplementary files format and content: Tab delimited data file included raw counts for each sample

organism: Tribolium castaneum

source_name: Fat body

extract_protocol:
Total RNA extraction using TRIzol® Reagent (Invitrogen, USA). To remove DNA contamination, samples were treated with DNase I (Qiagen, Germany).
The preprocessed reads of the samples were then aligned to the reference genome of T. castaneum (genome assembly version = Tcas5.2, GeneBank assembly identifier = GCF_000002335.3).

tag: developmental stage

value: adult

tag: phenotype

value: Susceptible

value: Fat body

value: COS-treatment


title: pbap2-g_KO_4h

description: Library name: Sample1

value: ring


title: Subject 1, 12 days, Kit A

value: 4 C refrigeration, RNA extraction kit A


title: Subject 1, 8 days, Kit A


title: COS70FB2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 191

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_191
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 2, 24 hours, Kit A


title: ATAC_KCa_D7_Smarca5_722

value: pancreas

value: pancreatitis


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 190

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_190
sci-RNA-seq3
L1_rice_combined.RData


title: COS70FB1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 189

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_189
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 2, 0 hours, Kit A


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 002

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_002
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 1, 4 days, Kit A


title: pbap2-g_KO_8h

description: Library name: Sample2

value: ANKA

value: trophozoite


title: Subject 1, 48 hours, Kit B


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 188

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_188
sci-RNA-seq3
L1_rice_combined.RData


title: COSMT2

source_name: Malpighian tubules

value: Malpighian tubules


title: ATAC_KCa_D7_Rosa_805

value: control

value: no


title: ATAC_KCa_D7_Smarca5_546


title: COSMT3


title: ATAC_KCa_D7_Rosa_724


title: COSMT1


title: Subject 1, 48 hours, Kit A

value: Whole blood


title: ATAC_KCa_D7_Smarca5_770


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 186

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_186
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: CONTROL3

source_name: Whole body

value: Whole body


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 185

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_185
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 187

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_187
sci-RNA-seq3
L1_rice_combined.RData


title: B_OC43_72h

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

description: hNECs infected with OC43

data_processing:
Sequencing data (Fastq raw files) were imported into Partek Flow (version 10.0, build 10.0.23.0531; Partek Inc., St. Louis, MO, USA), quality-controlled, and thereafter processed.
Paired-end reads were trimmed based on the Phred quality score threshold of >20 and aligned to the human genome (hg38) with the STAR - 2.7.8a aligner.
Quantification was done using the transcript model Ensembl Transcripts release 104 v2, subsequently normalised by the median ratio method.
Differential expressed genes were identified with the DESeq2 package.
Genes were called differentially expressed if FDR < 0.005, and fold change ≥ 2 or ≤ -2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file include output of DESeq2 analysis of the virus-infected versus mock samples comparison (total counts per gene, FDR, fold change of gene expression).

source_name: Primary cells

growth_protocol: Primary human nasal epithelial cells (hNECs) cultured under air–liquid interface conditions were purchased from Epithelix and maintained in Mucilair cell culture medium (Epithelix). Cells were grown at 5% CO2, 37oC and infections with HCoV were conducted at 33°C.

extract_protocol:
RNA was harvested using the Rneasy Mini Plus Kit (Quiagen). A total of ~1ug of RNA was used for construction of sequencing libraries.
According to the manufacturers protocol (Novogene): Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000, according to effective library concentration and data amount.
Library preparation and sequencing was performed by Novogene (mRNA library preparation (poly A enrichment))

treatment_protocol: Before infection, hNECs were washed with serum-free DMEM (Gibco) for 10 min at 37oC to remove mucus. Cells were infected with 200 µL of virus-containing serum-free DMEM and incubated at 33oC for 1 h. Inoculum was then removed, and cells were washed twice.

value: Primary cells

value: Nasal epithelial cells

value: WT

tag: time


title: ATAC_KCa_D7_Rosa_543


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 184

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_184
sci-RNA-seq3
L1_rice_combined.RData


title: Subject 1, 0 hours, Kit A


title: CONTROL1

value: adult

value: Susceptible


title: CONTROL2


title: ATAC_KCa_D7_Smarca5_541


title: ATAC_KCa_D2_Smarca5_498


title: A_OC43_72h

description: hNECs infected with OC43


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 183

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_183
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_D2_Smarca5_411


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 182

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_182
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_D2_Smarca5_273


title: B_OC43_24h

description: hNECs infected with OC43


title: Bank2 Trbeta with T3 repeat2

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

description: Library name: RUN66 lib8

library_source: other

data_processing:
Single end reads (>0.9 .106 reads/library) were trimmed from adaptor and plasmid sequences before mapping to the mouse genome (GRCm38/mm10 version. Bowtie2; Galaxy Version 2.4.2). Mapped data (.bam files) were converted to .bed files. Count tables were prepared by using BedTools . The Intersect intervals function (Galaxy Version 2.31.1+galaxy0) was used to identify overlaps between these BED files and the BED file corresponding to the transfected library, reporting the number of overlaps to produce the count files (processed data)
Reads which did not mapped only once (<20%) were binned.
Assembly: Mouse GRCm38/mm10 version
Supplementary files format and content: .bam files

molecule: other

source_name: HEK293 cell line

growth_protocol: Cells were transfected the day after seeding with plasmids and library DNA using the TransIT-Lt1 transfection reagent (Mirus Corporation, Madison WI, USA). Because the cells express endogenous receptors at very low level, expression vectors derived from pSG5 (Agilent Technology) were included in all experiments.

extract_protocol:
RNAs were extracted from transfected cells using the NucleoSpin RNA kit (Macherey Nagel) according to manufacturer instruction, including the recommended step of RNase-free DNase I treatment on the extraction column. The complete elimination of contaminant DNA from purified RNA was achieved by repeating the same procedure. cDNAs were prepared from 1 mg of RNA (M-MLV reverse transcriptase, Promega) using random hexamers (Eurogentec) as primers in a final volume of 20 mL. Reactions were stopped by the addition of EDTA (1 mM final) and the products diluted (1/4) with water. A PCR reaction was performed using the library amplification primers to verify after agarose gel electrophoresis the amplification of amplicons.
The resulting mixture of amplicons were then sequenced on a Miseq sequencer (Illumina Microkit V2 300 cycles) using the Illumina Nextera V2 index kit

treatment_protocol: T3 (Sigma Aldrich) was added 6 hours later (10-8M final) and cells were harvested the following day

value: HEK293 cell line

value: Kidney


title: Bank2 Trbeta no T3 repeat2

description: Library name: RUN66 lib7

value: No treatment


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 181

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_181
sci-RNA-seq3
L1_rice_combined.RData


title: A_OC43_24h

description: hNECs infected with OC43


title: ATAC_KCa_D7_Rosa_717

value: pancreas

value: pancreatitis


title: ATAC_KCa_D2_Smarca5_80


title: Bank2 Tralpha with T3

description: Library name: RUN66 lib6


title: B_229E_72h

description: hNECs infected with 229E


title: Subject 1, 0 hours, Kit B

value: 4 C refrigeration, RNA extraction kit B


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 180

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_180
sci-RNA-seq3
L1_rice_combined.RData


title: Bank2 Tralpha no T3

description: Library name: RUN66 lib5


title: ATAC_KCa_D2_Smarca5_61


title: A_229E_72h

description: hNECs infected with 229E


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 179

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_179
sci-RNA-seq3
L1_rice_combined.RData


title: B_229E_24h

description: hNECs infected with 229E


title: Bank1 Trbeta no T3 repeat2

description: Library name: RUN66 lib3


title: ATAC_KCa_D2_Rosa_495


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 177

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_177
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_D2_Rosa_258


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 178

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_178
sci-RNA-seq3
L1_rice_combined.RData


title: B_Mock

description: hNECs uninfected

value: Uninfected


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 176

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_176
sci-RNA-seq3
L1_rice_combined.RData


title: Bank1 Tralpha with T3 repeat2

description: Library name: RUN66 lib2


title: ATAC_KCa_D2_Rosa_85

value: control


title: A_Mock

description: hNECs uninfected


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 175

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_175
sci-RNA-seq3
L1_rice_combined.RData


title: Bank1 Tralpha no T3 repeat2

description: Library name: RUN66 lib1


title: ATAC_KCa_D2_Rosa_79

value: no


title: Bank2 LXRa with T-compound

description: Library name: RUN42 lib4

value: T-compound


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 174

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_174
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: Bank2 LXRa no T-compound

description: Library name: RUN42 lib3


title: ATAC_KCa_24h_Smarca5_376


title: L1EGK0901977--NC3

city: Shanghai

first: Yuan

last: Zhang

state: Shanghai

address: No.910 Hengshan Road

institute: The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
The quantification and quality of total RNA was checked by Nanodrop2000 (NanoDrop, USA) and Bioanalyzer 2100 (Agilent Technologies, USA)
Sequence reads were trimmed for adaptor sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: GRCh38
Supplementary files format and content: file includes raw counts for each sample
Supplementary files format and content: file includes FKPM values for each sample

source_name: cell line

extract_protocol:
The cells was cracked with Trizol reagent.
Sequencing libraries were generated using NEB Multiplex Small RNA Library Prep Set for Illumina NovaSeq 6000 (BioLabs, New England).

value: cell line

value: HTR8 cell line

value: trophocyte

value: RNA

value: no treatment


title: ATAC_KCa_24h_Smarca5_373


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 172

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_172
sci-RNA-seq3
L1_rice_combined.RData


title: L1EGK0901976--NC2


title: Bank2 Trbeta with T3 repeat1

description: Library name: RUN42 lib2


title: ATAC_KCa_24h_Smarca5_274


title: Bank1 Trbeta with T3 repeat2

description: Library name: RUN66 lib4


title: ATAC_KCa_D2_Rosa_499


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 173

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_173
sci-RNA-seq3
L1_rice_combined.RData


title: A_229E_24h

description: hNECs infected with 229E

value: Primary cells

value: Nasal epithelial cells

value: WT


title: Bank1 Trbeta with T3 repeat1

description: Library name: RUN25 lib4

value: HEK293 cell line

value: Kidney


title: L1EGK0901974--ExoC4

value: exosome co-culcure


title: ATAC_KCa_24h_Smarca5_73

value: pancreas

value: pancreatitis


title: L1EGK0901975--NC1


title: Bank1 Trbeta no T3 repeat1

description: Library name: RUN25 lib3

value: No treatment


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 170

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_170
sci-RNA-seq3
L1_rice_combined.RData


title: L1EGK0901973--ExoC3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 169

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_169
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_24h_Rosa_372

value: control

value: no


title: L1EGK0901978--NC4


title: Bank1 Tralpha with T3 repeat1

description: Library name: RUN25 lib2


title: ATAC_KCa_24h_Rosa_266


title: L1EGK0901972--ExoC2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 168

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_168
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: ATAC_KCa_24h_Rosa_247


title: L1EGK0901971--ExoC1

value: cell line


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 167

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_167
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_24h_Rosa_133


title: Bank2 Trbeta no T3 repeat1

description: Library name: RUN42 lib1


title: SiG_rep3

city: Mineola

first: Qing

middle: Robert

last: Miao

state: NY

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

data_processing:
Sequencing reads were processed through the MAPR-Seq Differential expression analysis completed with DESeq2
Assembly: hg19
Supplementary files format and content: Rawcounts_HG_NS_siGlut1.csv

source_name: HBMEC

growth_protocol: Human brain microvascular endothelial cells were purcashed from Cell Systems (ACBRI376) and kept in complete growth mediuem from Cell Systems (4Z0-500).

extract_protocol:
RNA were isolated using Qiagen Rneasy Mini kit (74106). Libraries were prepared according to manufacturer’s protocols (TruSeq stranded mRNA, Illumina, San Diego, CA, USA)
RNA libraries fro RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were transfected with siRNA for 48 hours

value: HBMEC

value: Human Brain Microvascular Endothelial Cells


title: ATAC_KCa_24h_Rosa_72


title: SiG_rep2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 165

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_165
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 171

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_171
sci-RNA-seq3
L1_rice_combined.RData


title: PBMC healthy n°4

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

institute: Institut Imagine

description:
Chromium Single Cell 3′ Library & Gel Bead Kit v.3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome (hg38), using the CellRanger Pipeline v6.0
Unfiltered RNA UMI counts were loaded into Seurat v4 for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with with low number of features (Filters were defined based on the batch : AGSexp1 and AGSexp2: nFeature <250 ; AGSexp3 <500) or a mitochondrial content higher than 20%.
Data from each sample were normalized using sctransform, before batch correction using Seurat’s FindIntegratedAnchors, on the 3000 most variable features. To avoid over-aligning samples, a reciprocal principal component analysis (PCA) was used to find integration anchors
On the resulting integrated datasets, we computed the PCA on the 3000 most variable genes, before computing a UMAP on 20 PCs. Community detection was performed using the graph-based modularity-optimization Louvain algorithm from Seurat’s FindClusters function with a 1.2 resolution.
Cell types labels were assigned to resulting clusters based on a manually curated list of marker genes as well as previously defined signatures of the well-known PBMCs subtypes.(Monaco et al., 2019)
Assembly: hg38
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (2200 rpm or 974g without break for 30 minutes) using Ficoll (Eurobio Scientific, Les Ulis, France). After centrifugation, the pellet was resuspended in Phosphate-buffered saline (PBS) (Thermo Fisher scientific, Illkirch, France) and cells were centrifuged at 1500 rpm (453g)  for 5 minutes. Finally, the pellet was frozen in a medium containing 90% of Fetal Bovine Serum (FBS) (GIBCO, Thermo Fisher scientific, Illkirch, France) and 10% of dimethyl sulfoxide (DMSO) (Sigma Aldrich, St. Quentin Fallavier, France), and stored in liquid nitrogen.  PBMCs were thawed according to 10X Genomics protocol.
The scRNA-seq libraries were generated using Chromium Single Cell 3′ Library & Gel Bead Kit v.1 (for AGSexp1 and AGSexp2) or v.3 (for AGSexp3) (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1000 cells/µL in PBS+0,04% and 20,000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR

value: Blood

value: healthy

tag: Sex

value: F

tag: age (year)

tag: original name


title: PBMC healthy n°5

value: M


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 166

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_166
sci-RNA-seq3
L1_rice_combined.RData


title: SiG_rep1


title: PBMC healthy n°3

description:
Chromium Single Cell 3′ Library & Gel Bead Kit v.1
10x Genomics


title: NS_rep3

value: Non-silence


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 164

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_164
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_8h_Smarca5_250


title: ATAC_KCa_8h_Rosa_261


title: PBMC healthy n°1, rep2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 163

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_163
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 162

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_162
sci-RNA-seq3
L1_rice_combined.RData


title: NS_rep2


title: Bank1 Tralpha no T3 repeat1

description: Library name: RUN25 lib1

value: HEK293 cell line


title: ATAC_KCa_8h_Rosa_236


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 161

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_161
sci-RNA-seq3
L1_rice_combined.RData


title: HGSiG_rep3

value: HighGlucose


title: PBMC COPA patient n°2

value: COPA


title: PBMC healthy n°1, rep1


title: ATAC_KCa_0h_Smarca5_218

value: pancreas

value: acinar


title: PBMC healthy n°2


title: ATAC_KCa_0h_Rosa_212


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 158

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_158
sci-RNA-seq3
L1_rice_combined.RData


title: PBMC AGS6 patient n°2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 160

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_160
sci-RNA-seq3
L1_rice_combined.RData


title: HGNS_rep3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 157

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_157
sci-RNA-seq3
L1_rice_combined.RData


title: ATAC_KCa_0h_Smarca5_213


title: The kidney  of C57BL/6 mice, 18 month with ID 2

city: Cheng Du

first: Yan

last: Pan

address: Northern Jianshe Road

institute: University of Electronic Science and Technology of China

description: Library name: Kidney_O_2

data_processing:
Use internal software SOAPnuke to filter reads: 1)Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%;3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read).(version：v1.5.2)
Use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.(Version: v2.0.4)
Mapped clean reads to reference using Bowtie2(Version: v2.2.5)
Calculate gene expression level with  RSEM(Version: v1.2.12)
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

extract_protocol:
Perfusion with 0.1mol/L PB for cardiac perfusionis , wait for the liver to turn white, quickly obtain the cerebral cortex, hippocampus, kidneys tissue samples , stored with 1 ml of RNA later cryovials and transfer with dry ice. Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTM to identify the purity of the RNA samples.
The library was constructed using classical OligodT magnetic beads to enrich mRNA.

value: kidney

value: 18 month


title: NS_rep1

value: control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 156

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_156
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

value: seedling


title: ATAC_KCa_8h_Smarca5_262

source_name: pancreas

value: pancreatitis

value: no


title: PBMC COPA patient n°1


title: HGSiG_rep2

value: HBMEC

value: Human Brain Microvascular Endothelial Cells


title: The kidney  of C57BL/6 mice, 10 month with ID 3

description: Library name: Kidney_M_3

value: 10 month


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 159

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_159
sci-RNA-seq3
L1_rice_combined.RData

source_name: seedling


title: HGSiG_rep1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 154

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_154
sci-RNA-seq3
L1_rice_combined.RData


title: HGNS_rep2


title: PBMC AGS6 patient n°1

value: Blood

value: F


title: The kidney  of C57BL/6 mice, 18 month with ID 3

description: Library name: Kidney_O_3


title: PBMC AGS2 patient n°2


title: PBMC AGS5 patient n°2, rep2

value: M


title: HGNS_rep1

value: Non-silence


title: The kidney  of C57BL/6 mice, 10 month with ID 1

description: Library name: Kidney_M_1


title: The kidney  of C57BL/6 mice, 18 month with ID 1

description: Library name: Kidney_O_1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 155

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_155
sci-RNA-seq3
L1_rice_combined.RData


title: PBMC AGS2 patient n°1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 152

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_152
sci-RNA-seq3
L1_rice_combined.RData


title: PBMC AGS5 patient n°2, 1 month RTI treatment

value: 1 month RTI


title: Hs578T_H3K27ac_ChIPSeq

city: San Francisco

first: Denise

middle: Paula

last: Muñoz

state: California

address: 2340 Sutter St.

department: Hematology/Oncology

institute: University of California, San Francisco

data_processing:
Bowtie 2 (2.2.9) - option: very sensitive
MACS2 (2.1.1.20160309) - Peaks were called using the following parameters: keep-dup 1, with a q value of 0.05, lower m fold bound of 5, upper m fold bound of 50 and band with of 300
Signal files (bigwig) were generated with deeptools bamcompare (3.3.2.0.0) by substracting library-size normalized (readCount) Input sample (bam file) from library-size normalized IP sample (bam file) in 25bp-bins, extending the reads to the average fragment size informed by MACS for each library. Negative values were converted to 0.
Assembly: hg19
Supplementary files format and content: Signal files in bigwig format, contains IP-Input normalized signal for 25bp windows across the whole genome

source_name: Breast cancer cells

growth_protocol: HCC1569 and BT483 cell lines were grown in RPMI supplemented with 10% FBS and 1X Penicillin/Streptomycin; BT474 and Hs578T cell lines were grown in DMEM supplemented with 10% FBS and 1X Penicillin/Streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of indexed Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The libraries were quantified using the Kapa Biosystems quantification kit SYBR Fast ABI Prism, and between 6-8 samples were pooled and sequenced on a HiSeq4000 with 50-base single reads.

value: Breast cancer cells

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: Hs578T_input DNA


title: The kidney  of C57BL/6 mice, 10 month with ID 2

description: Library name: Kidney_M_2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 153

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_153
sci-RNA-seq3
L1_rice_combined.RData


title: BT483_H3K27ac_ChIPSeq


title: BT483_input DNA


title: PBMC AGS5 patient n°2, rep1


title: BT474_H3K27ac_ChIPSeq


title: BT474_input DNA


title: The hippocampus  of C57BL/6 mice, 18 month with ID 3

description: Library name: Hipp_O_3

source_name: hippocampus

value: hippocampus


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 148

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_148
sci-RNA-seq3
L1_rice_combined.RData


title: PBMC AGS5 patient n°1, 5 month RTI treatment

value: 5 month RTI


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 151

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_151
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 150

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_150
sci-RNA-seq3
L1_rice_combined.RData


title: H441 cells, FOXA2 Rep 3

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore (version 0.4.2) with "-q 20 --stringency 1 --length 20 -clip_R1 2 -clip_R2 2".
Reads were then aligned to hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
Gene expression was counted using htseq-count with "-s no -m union -t exon".
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include gene expression count values for each sample

growth_protocol: H441 human lung papillary adenocarcinoma 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 TRIzol Reagent (Thermo Fisher) amd purified using Rneasy MinElute Cleanup kit (Qiagen). Sequencing libraries were constructed by Cincinnati Children's Hospital Medical Center (CCHMC) DNA Sequencing and Genotyping Core.
RNA libraries for RNA-seq were prepared by CCHMC DNA Sequencing and Genotyping Core.

treatment_protocol: H441 cells were infected with lentivirus that carries empty control or rat Foxa2 (PGK promoter driven).

value: lung papillary adenocarcinoma cells

value: rat FOXA2 lentivirus

value: lentivirus infection

value: More than 1 week


title: The kidney  of C57BL/6 mice, 2 month with ID 1

description: Library name: Kidney_Y_1

value: kidney

value: 2 month


title: The hippocampus  of C57BL/6 mice, 18 month with ID 1

description: Library name: Hipp_O_1

value: 18 month


title: The kidney  of C57BL/6 mice, 2 month with ID 3

description: Library name: Kidney_Y_3


title: HCC1569_input DNA


title: H441 cells, Control Rep 2

institute: Cincinnati Children's Hospital Medical Center

value: Control lentivirus


title: H441 cells, FOXA2 Rep 1


title: The hippocampus  of C57BL/6 mice, 10 month with ID 3

description: Library name: Hipp_M_3

value: 10 month


title: HCC1569_H3K27ac_ChIPSeq


title: The hippocampus  of C57BL/6 mice, 18 month with ID 2

description: Library name: Hipp_O_2


title: H441 cells, Control Rep 1


title: PPT 2

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

data_processing:
FastQC
Trimmomatic
FastQC
Kallisto
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files with RAWCOUNTS/TPM/FPKM values.

source_name: PC3 Cells

growth_protocol: PC3 cells were maintained in RPMI 1640 with penicillin, streptomycin, sodium pyruvate, and 10% fetal bovine serum.

extract_protocol:
RNA were purified using the RNeasy plus purification kit from QIAGEN.
NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina

treatment_protocol: PC3 cells were plated in RPMI 1640 media with no phenol red enriched with 5% charcoal stripped serum, sodium pyruvate, penicillin and streptomycin and left to grow during 48h to allow steroid deprivation. Then, media was changed and the cells were treated with either: vehicle (mix of 96% ethanol and DMSO), E2 (10 nM), PPT (1 nM) or DPN (4.25 nM).

tag: cell lines

value: 1 nM PPT


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 149

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_149
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: H441 cells, FOXA2 Rep 2


title: PPT 3


title: 20210819_AMO1_DR-KO_d1_NC-1

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
Alignment done with STAR against hg19
FASTQC was used to check quality of fastq files
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

extract_protocol:
Total RNA was extracted using trisol according to manufacturer protocol.
RNA libraries for RNA-seq were prepared using stranded ployA selected mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Control


title: The kidney  of C57BL/6 mice, 2 month with ID 2

description: Library name: Kidney_Y_2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 147

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_147
sci-RNA-seq3
L1_rice_combined.RData


title: E2 3

value: 10 nM E2


title: The hippocampus  of C57BL/6 mice, 2 month with ID 3

description: Library name: Hipp_Y_3


title: H441 cells, Control Rep 3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 146

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_146
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 142

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_142
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 145

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_145
sci-RNA-seq3
L1_rice_combined.RData


title: The hippocampus  of C57BL/6 mice, 10 month with ID 2

description: Library name: Hipp_M_2


title: 20210819_AMO1_DR-KO_d1_ASO1-2


title: PPT 1


title: The hippocampus  of C57BL/6 mice, 2 month with ID 2

description: Library name: Hipp_Y_2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 144

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_144
sci-RNA-seq3
L1_rice_combined.RData


title: The hippocampus  of C57BL/6 mice, 2 month with ID 1

description: Library name: Hipp_Y_1


title: The hippocampus  of C57BL/6 mice, 10 month with ID 1

description: Library name: Hipp_M_1


title: 20210819_AMO1_DR-KO_d1_NC-2


title: The cortex  of C57BL/6 mice, 18 month with ID 3

description: Library name: Cortex_O_3

source_name: cortex

value: cortex


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 139

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_139
sci-RNA-seq3
L1_rice_combined.RData


title: E2 2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 143

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_143
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 140

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_140
sci-RNA-seq3
L1_rice_combined.RData


title: 20210819_AMO1_DR-KO_d1_ASO1-1


title: E2 1


title: M28z-KITv CAR-T cells stimulated for 24 hours_rep 3

first: Yuquan

last: Xiong

address: 1250 1st Avenue, Room S-1211

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) were mapped to the target genome using the STAR aligner, which maps reads genomically and resolves reads across splice junctions. We used the 2-pass mapping method, in which the reads are mapped twice. The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions, and a second mapping pass was performed. We then computed the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases. The raw count matrixes generated by HTSeq were then processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq), which is used to both normalize the full data set and analyze differential expression between sample groups
Assembly: hg19
Supplementary files format and content: Proj_B-101-173_htseq_all_samples.txt
Supplementary files format and content: Proj_B-101-173_counts_scaled_DESeq.xlsx

source_name: M28z-KITv CAR-T

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

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN), according to the instructions provided by the manufacturer. After RiboGreen RNA quantification and quality control using an Agilent Bioanalyzer.
libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina), followed by sequencing (60 million 50 bp paried-end reads) on Illumina NovaSeq 6000.

value: CD8+ T cells

value: M28z-KITv CAR-T

value: stimulated for 24 hours


title: The cortex  of C57BL/6 mice, 18 month with ID 1

description: Library name: Cortex_O_1


title: CTL 3

value: 96 percent  Ethanol + DMSO


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 141

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_141
sci-RNA-seq3
L1_rice_combined.RData


title: DPN 3

value: 4.25 nM DPN


title: SKOV3

city: Jinan

first: Hui

state: China

address: 107 West Wenhua Road

institute: Qilu Hospital, Shandong University

data_processing:
Agilent 2100 bioanalyzer detected the insert size(250-300bp)
qPCR was used to measure the library concerntration to keep it>2nM
Illumina PE150(Pair end 150 bp)system seq
clean reads were mapping via Hisat2
Assembling by Stringtie and Cuffmerge
quantified by  StringTie
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: SKOV3 cells were maintained in McCoy’s 5A with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was harvested via Trizol method for  the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using RibomInus Transcriptome Isolation Kit（Invitrogen）  following manufacturer's protocols.

treatment_protocol: SKOV3 cells were treated with PARP inhibitor（Olaparib）in half-IC50 concentration continuously for at least 3 months to induce the PARPi-resistant cell line

value: human ovarian cancer cell

value: WT


title: CTL 2


title: DPN 2


title: M28z-KITv CAR-T cells stimulated for 24 hours_rep 1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 136

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_136
sci-RNA-seq3
L1_rice_combined.RData


title: CTL 1


title: The cortex  of C57BL/6 mice, 18 month with ID 2

description: Library name: Cortex_O_2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 138

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_138
sci-RNA-seq3
L1_rice_combined.RData


title: SKOV3_OR

value: PARP inhibitor therapy


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 135

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_135
sci-RNA-seq3
L1_rice_combined.RData


title: Sep_H_elute

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

description: processed data file: Count_Table_Elisa_Experiment.xlsx

data_processing:
library strategy: DNA-seq (PCR product sequencing)
The HiSeq Real Time Analysis software (RTA 1.12) was used for processing image files, the Illumina CASAVA_v1.8.2 was used for converting binary base calls and qualities to fastq format.
The fastq files for each lane were concatenated and aligned with Phix using Bowtie2
Data were filtered using the following procedure: PhiX mapped reads were filtered, the remaining sequence reads were adapter trimmed and de-barcoded based on barcode indices with 0-mismatch, 1-mismatch or 2-mismatch.
Duplicate reads were collapsed to obtain unique read counts in each instance. The read counts for each barcode oligos are calculated to get overall count and unique count.
Clustering analysis was performed using 1-Pearson correlations with average linking
Genome_build: None
Supplementary_files_format_and_content: Each Excel file contains the count table to measure the abundance of the oligonucleotides sequenced for each sample in  a specific experiment.

source_name: Oligos_Elisa Experiment

extract_protocol:
Antibody conjugates bearing a cleavable covalently attached anchor oligonucleotides were generated by commercially available hydrazine-carbonyl conjugation chemistry.  Synthetic signature oligonucleotides comprised of all necessary Illumina adapter sequences and an extended barcode were hybridized to the universal anchor DNA sequence.
Following cleavage and isolation of the oligonucleotide complexes, libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.  Following preamplification, the final purified products are quantitated by qPCR before cluster generation and sequencing.

tag: sample group/info.

value: Her2 ELISA experiment 4

tag: antibody binding

value: recombinant Her2 protein ELISA

tag: molecule type

value: Oligos; PCR product


title: The cortex  of C57BL/6 mice, 2 month with ID 3

description: Library name: Cortex_Y_3

tag: tissue

value: 2 month


title: M28z-KITv CAR-T cells stimulated for 24 hours_rep 2

city: New York

tag: cell type

tag: cell line


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 134

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_134
sci-RNA-seq3
L1_rice_combined.RData

tag: age


title: M28z CAR-T cells stimulated for 24 hours_rep 3

source_name: M28z CAR-T

value: M28z CAR-T

tag: treatment


title: Sep_G_elute

value: Her2 ELISA experiment 3


title: Col_H_elute

value: Her2 ELISA experiment 2


title: The cortex  of C57BL/6 mice, 10 month with ID 1

description: Library name: Cortex_M_1

tag: genotype

value: 10 month


title: DPN 1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 137

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_137
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: M28z CAR-T cells stimulated for 24 hours_rep 2

value: CD8+ T cells


title: M28z-KITv CAR-T cells_rep3

value: M28z-KITv CAR-T

value: non-stimulated


title: The cortex  of C57BL/6 mice, 2 month with ID 1

description: Library name: Cortex_Y_1

value: cortex


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 133

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_133
sci-RNA-seq3
L1_rice_combined.RData


title: Col_G_elute

value: Her2 ELISA experiment 1


title: The cortex  of C57BL/6 mice, 10 month with ID 2

description: Library name: Cortex_M_2


title: The cortex  of C57BL/6 mice, 2 month with ID 2

description: Library name: Cortex_Y_2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 131

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_131
sci-RNA-seq3
L1_rice_combined.RData


title: The primary neuron of C57BL/6 mice, Etoposide 10 Days with ID3

description: Library name: N_E3

data_processing:
Use internal software SOAPnuke to filter reads: 1)Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%;3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read).(version：v1.5.2)
Use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.(Version: v2.0.4)
Mapped clean reads to reference using Bowtie2(Version: v2.2.5)
Calculate gene expression level with  RSEM(Version: v1.2.12)
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary neuron

extract_protocol:
Remove the medium, wash the cells with 1 ml of PBS, add 1 ml of RNA extract and freeze and transfer on dry ice.Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTM to identify the purity of the RNA samples.
The library was constructed using classical OligodT magnetic beads to enrich mRNA.

value: primary neuron

value: Control(DMSO)


title: The cortex  of C57BL/6 mice, 10 month with ID 3

description: Library name: Cortex_M_3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 132

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_132
sci-RNA-seq3
L1_rice_combined.RData


title: GM6B

description: processed data file: Count_Table_Her2_Singleplex_Experiment.xlsx

source_name: Oligos_Her2 Experiment - Singleplex

value: Her2 tissue SINGLEPLEX (703); TMAs 6.501-6.508

value: synthetic oligo on human FFPE tissue


title: M28z-KITv CAR-T cells_rep2


title: M28z-KITv CAR-T cells_rep1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 130

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_130
sci-RNA-seq3
L1_rice_combined.RData


title: The primary neuron of C57BL/6 mice, Etoposide 10 Days with ID2

description: Library name: N_E2

value: WT


title: M28z CAR-T cells_rep3


title: GM5B

value: Her2 tissue SINGLEPLEX (703); TMAs 5.501-5.508

value: Oligos; PCR product


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 129

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_129
sci-RNA-seq3
L1_rice_combined.RData


title: M28z CAR-T cells stimulated for 24 hours_rep 1

value: M28z CAR-T

value: stimulated for 24 hours


title: GM4B

value: Her2 tissue SINGLEPLEX (703); TMAs 4.501-4.508


title: M28z CAR-T cells_rep2


title: M28z CAR-T cells_rep1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 127

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_127
sci-RNA-seq3
L1_rice_combined.RData


title: The primary neuron of C57BL/6 mice, Control(DMSO)  10 Days with ID2

description: Library name: N_D2

value: Etoposide


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 128

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_128
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: The primary neuron of C57BL/6 mice, Control(DMSO)  10 Days with ID3

description: Library name: N_D3


title: GM3B

value: Her2 tissue SINGLEPLEX (703); TMAs 3.501-3.508


title: HEK293+V279del

city: Shoufeng Township

first: Hsiang-Chin

last: Chen

state: Hualien

address: Daxue Road

department: Department of Life science

country: Taiwan

institute: National Dong-Hwa University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen),  total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HEK 293 cells overexpressed V2R or V279del with/wiout the treatment of AVP( 1ug, 8 hrs)

value: embryonic kidney cells

value: Overexpression of V279del


title: HEK293+V279del+AVP

value: Overexpression of V279del+AVP


title: The primary neuron of C57BL/6 mice, Control  10 Days with ID3

description: Library name: Neuron_mCherry3

value: mCherry


title: GM2B

value: Her2 tissue SINGLEPLEX (703); TMAs 2.501-2.508


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 126

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_126
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 125

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_125
sci-RNA-seq3
L1_rice_combined.RData


title: ST_GM5A

description: processed data file: Count_Table_Her2_Multiplex_Experiment.xlsx

source_name: Oligos_Her2 Experiment - Multiplex

value: separate tissue experiment with a spike in standard curve


title: The primary neuron of C57BL/6 mice, Etoposide 10 Days with ID1

description: Library name: N_E1

value: primary neuron

value: Control(DMSO)


title: The primary neuron of C57BL/6 mice, Control  10 Days with ID2

description: Library name: Neuron_mCherry2

value: WT


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 124

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_124
sci-RNA-seq3
L1_rice_combined.RData


title: HEK293+V2R+AVP

value: Overexpression of V2R+AVP


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 123

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_123
sci-RNA-seq3
L1_rice_combined.RData


title: HEK293+AVP

value: AVP


title: GM6A

value: Her2 tissue in multiplex (703); TMAs 6.501-6.508

value: synthetic oligo on human FFPE tissue

value: Oligos; PCR product


title: GM5A

value: Her2 tissue in multiplex (703); TMAs 5.501-5.508


title: The primary neuron of C57BL/6 mice, Control(DMSO)  10 Days with ID1

description: Library name: N_D1

value: Etoposide


title: The primary neuron of C57BL/6 mice, Control  10 Days with ID1

description: Library name: Neuron_mCherry1


title: HEK293


title: The primary neuron of C57BL/6 mice, over-expression H-Ras(G12V)  10 Days with ID3

description: Library name: Neuron_G12V3


title: GM4A

value: Her2 tissue in multiplex (703); TMAs 4.501-4.508


title: HEK293+V2R

value: embryonic kidney cells

value: Overexpression of V2R


title: The primary neuron of C57BL/6 mice, over-expression H-Ras(G12V)  10 Days with ID2

description: Library name: Neuron_G12V2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 121

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_121
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: The primary neuron of C57BL/6 mice, over-expression H-Ras(G12V)  10 Days with ID1

description: Library name: Neuron_G12V1


title: GM3A

value: Her2 tissue in multiplex (703); TMAs 3.501-3.508


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 120

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_120
sci-RNA-seq3
L1_rice_combined.RData


title: GM1B

value: Her2 tissue SINGLEPLEX (703); TMAs 1.501-1.508


title: GM2A

value: Her2 tissue in multiplex (703); TMAs 2.501-2.508


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 119

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_119
sci-RNA-seq3
L1_rice_combined.RData


title: HCT116 cells, shWDR43, rep1

city: Guangzhou

first: Ziyang

last: Wang

state: Guangdong

address: 58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HCT116 cells were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were infected with shNC, WDR43 knockdown lentiviruses for 48 h, and then screened by puromycin for 3 days.

value: colorectal carcinoma cells

value: WDR43 knockdown

value: transfected with shWDR43


title: Radiation,Day180-4

city: chengdu

first: lixin

last: gong

address: No. 4, North Fourth Section, Second Ring Road

institute: The Second Affiliated Hospital of Chengdu Medical College Nuclear Industry 416 Hospital

data_processing:
After obtaining the clean reads, we use Bowtie2 to align the clean reads to the reference genome sequence.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw count for each Sample
Supplementary files format and content: tab-delimited text file includes raw RPKM values foe each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

value: Lung

tag: time point

tag: agent

value: Radiation


title: GM1A

value: Her2 tissue in multiplex (703); TMAs 1.501-1.508


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 122

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_122
sci-RNA-seq3
L1_rice_combined.RData

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.


title: Radiation,Day180-3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 118

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_118
sci-RNA-seq3
L1_rice_combined.RData


title: Mil_126b

description: processed data file: Count_Table_Tissue_Experiment_Two.xlsx

source_name: Oligos_Tissue Experiment 2

value: synthetic oligo on human FFPE tissue


title: HCT116 cells, shNC2 rep1

value: Control

value: transfected with shNC


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 117

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_117
sci-RNA-seq3
L1_rice_combined.RData


title: Mil_115b

value: Oligos; PCR product


title: RBEC_OGDR_plus_DMT_plus_BD1063_6

city: Szeged

first: Maria

last: Deli

address: Temesvari krt. 62.

department: Institute of Biophysics

country: Hungary

institute: HUN-REN Biological Research Centre

description: Library name: DMT_plus_BD6

data_processing:
Unprocessed sequencing reads were adapter-trimmed and quality-trimmed using Cutadapt (3.4). FastQC (0.11.9) was used to assess the quality of sequencing reads.
Cleaned reads were mapped to the reference genome using STAR (2.7.10a), allowing for spliced alignments.
Quantification of mapped reads to each gene was performed STAR (2.7.10a]) and RSEM (1.3.3).
Raw counts were TPM-normalized by dividing each count with the sum of all counts for each sample multiplied by one million
Differential expression analysis was performed using DESeq2 (version 1.38)
Assembly: Rnor_6.0
Supplementary files format and content: Excel file including all raw counts for each sample
Supplementary files format and content: Excel file including all TPM normalized counts for each sample

organism: Rattus norvegicus

source_name: primary brain endothelial cell

extract_protocol:
Total RNA was extracted by column based extraction kit (Zymo)
RNA-Seq libraries (NEBNext Ultra II Directional) were prepared according to the manual of the manufacturers. Summarized, enriched poly-Adenylated mRNA is fragmented, followed by cDNA synthesis using random hexamers. The cDNA fragments undergo end repair, A-tailing followed by ligation of Illumina P5 and P7 adapters. After PCR amplification using a minimum number of cycles, purification by SPRI beads, the quality of the libraries was controlled for size-distribution and quantity. Sequencing was performed on an Illumina NEXTSEQ 500 instrument with 1x75 bps.

value: primary brain endothelial cell


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 116

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_116
sci-RNA-seq3
L1_rice_combined.RData


title: Radiation,Day180-1


title: HCT116 cells, shWDR43, rep2


title: RBEC_OGDR_plus_DMT_plus_BD1063_5

description: Library name: DMT_plus_BD5


title: Mil_104b


title: Radiation,Day90-4


title: Mil_93b


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 115

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_115
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_OGDR_plus_DMT_plus_BD1063_4

description: Library name: DMT_plus_BD4


title: RBEC_OGDR_plus_DMT_plus_BD1063_3

description: Library name: DMT_plus_BD3


title: Radiation,Day90-2


title: Mil_82b


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 114

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_114
sci-RNA-seq3
L1_rice_combined.RData


title: Mil_71b


title: Radiation,Day90-3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 113

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_113
sci-RNA-seq3
L1_rice_combined.RData


title: HCT116 cells, shNC2 rep2


title: RBEC_OGDR_plus_DMT_plus_BD1063_1

description: Library name: DMT_plus_BD1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 111

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_111
sci-RNA-seq3
L1_rice_combined.RData


title: Radiation,Day90-1


title: Radiation,Day14-4


title: Radiation,Day180-2


title: Mil_5

description: processed data file: Count_Table_Tissue_Experiment_One.xlsx

source_name: Oligos_Tissue Experiment 1


title: RBEC_OGDR_plus_DMT_5

description: Library name: DMT5


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 110

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_110
sci-RNA-seq3
L1_rice_combined.RData


title: Radiation,Day14-3


title: RBEC_OGDR_plus_DMT_4

description: Library name: DMT4


title: Mil_4


title: Mil_3


title: Radiation,Day14-2


title: Radiation,Day14-1


title: RBEC_OGDR_plus_DMT_3

description: Library name: DMT3


title: RBEC_OGDR_plus_DMT_2

description: Library name: DMT2


title: RBEC_OGDR_plus_DMT_plus_BD1063_2

description: Library name: DMT_plus_BD2


title: Mil_2


title: Mil_1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 112

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_112
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_OGDR_plus_DMT_1

description: Library name: DMT1


title: Control,Day180-4


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 107

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_107
sci-RNA-seq3
L1_rice_combined.RData


title: CRISPR_T5

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
For ChIP-seq assays, raw FASTQ ﬁles were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. For RNA-seq assays, the paired-end reads were aligned to hg38 using STAR. After calculating raw gene expression levels (raw read counts) with FeatureCounts, normalized profiling data were obtained with DESeq2 for differential expression analysis.
For CRISPR screening, the raw FASTQ ﬁles were demultiplexed using Geneious 7.0 (Biomatters Inc.) and processed such that they contained only the unique sgRNA sequence. The designed barcode sequences from the library were assembled into a mapping reference sequence to align the processed reads to the library. The reads were then aligned to the reference sequence using the "Map to Reference" function in Geneious 7.0. After alignment, the number of uniquely aligned reads for each library sequence was calculated. The number of reads of each unique sgRNA for a certain sample was normalized as follows: normalized read counts per unique barcode = reads per barcode/total reads for all barcodes in the sample × 10^6 + 1. The sgRNA score was generated and ranked according to the depletion or enrichment of the normalized sgRNA counts (Sequence_results_T_vs_C.xlsx).
For ChIP-seq assays, bam files were converted to BigWig files using deepTools.
For ChIP-seq assays, peaks were identified using the MACS2 peak caller with the following parameters: -t treatment -c input –f BAMPE –keep-dup all –g hs –q 0.01
Assembly: For RNA-seq and ChIP-seq assays, hg38. For CRISPR screening, the reads were aligned to the reference sequence of the library.
Supplementary files format and content: peak files were generated using MACS2.

source_name: liver

growth_protocol: HUH7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.  Methods.2009;48:240-8)；
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit.  Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 6000 platform (Illumina, CA, USA);  ChIP-seq was performed according to the manufacturer’s protocol (NEB, Shanghai, China). For CRISPR screening, Genomic DNA of day 0 cell samples and xenograft tumor samples were extracted with the Qiagen Blood & Cell Culture Midi Kit (Qiagen, Hilden, Germany). SgRNA cassettes were amplified from genomic DNA samples as the ﬁrst PCR, the amplicons resulting from the second PCR were extracted with beads (Beckman Coulter, USA), quantiﬁed, mixed, and sequenced using a NextSeq 500 instrument (Illumina, USA).

treatment_protocol: siRNAs targeting DDX41 and negative control siRNAs (NC) were procured from RiboBio (Guangzhou, China).  Cells were transfected with the specified targeted or control siRNA  using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA).  After 48 hours of transfection, the cells were collected for further experiments.HUH7 cells with stable overexpression of Flag-DDX41, Flag-RNASEH1-Mu (for R-ChIP assay), Flag-NR2C1, Flag-NR2C2 were collected for further experiments. For CRISPR screening, customized library containing 4992 sgRNAs specifically targeting 832 transcription factor (TF) and chromatin regulator (CR) genes (6 sgRNAs per gene), with 500 negative control sgRNAs and 12 positive control sgRNAs for 2 validated oncogenes. HUH7 cells were transduced with the pooled sgRNA lentiviral library at a low MOI value of 0.3. After 7 days of puromycin (Invitrogen, USA) selection (5 μg/ml), the surviving cells were considered to be the day 0 sample, and 3×10^7 of these cells were stored for further processing. The remaining cells were counted, and 1×10^7 cells per mouse were subcutaneously injected into NOD/Scidil2Rγ-/- (NSG) mice for xenograft tumor formation. Genomic DNA of day 0 cell samples (C1-C5) and xenograft tumor samples (T1-T5) were extracted and amplified for sequencing.

value: liver

value: HCC cells

value: HUH7 cell stable transfected with Cas9-GFP-Luc and sgRNA library lentivirus


title: Mil_6


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 105

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_105
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: RBEC_OGDR_6

description: Library name: CTR6


title: CRISPR_T4


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 104

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_104
sci-RNA-seq3
L1_rice_combined.RData


title: RBEC_OGDR_5

description: Library name: CTR5


title: CRISPR_T3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 109

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_109
sci-RNA-seq3
L1_rice_combined.RData


title: Control,Day180-1


title: RBEC_OGDR_4

description: Library name: CTR4