title: dvelB

first: Antonis

last: Rokas

address: VU Station B 35-1364

department: Biological Sciences

institute: Vanderbilt University

description: A. nidulans velB deletion mutant

data_processing:
Reads were mapped to the A. nidulans FGSC4 transcriptome using Tophat2 version 2.1.1 and the parameter “--max-intron-length 4000”.
The number of reads aligning to each gene was counted with HTseq-Count version 0.9.1.
Genome_build: FungiDB-32_AnidulansFGSCA4
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each gene in each sample

organism: Aspergillus nidulans

source_name: 2-day-old spores

growth_protocol: Conidia were inoculated onto solid minimal media with 1% glucose (MMG plates) and incubated for 48 h. Then, conidia were collected from plates using Miracloth (Calbiochem, San Diego, CA, USA) and stored at −80°C.

extract_protocol:
Total RNA from conidia was extracted using Trizol Reagent (Invitrogen, USA), according to the manufacturer’s instructions with modifications. To remove DNA contamination from the RNA samples, DNase I (Promega, USA) was added and then RNA was purified using an RNeasy Mini kit (Qiagen, USA).
RNA samples were submitted to the University of Wisconsin Gene Expression Center (Madison, WI, USA) for library preparation and sequencing. A strand-specific library was prepared using an Illumina TruSeq strand-specific RNA sample preparation system.


title: RNA-seq FKBPFV-HCF-1N DMSO rep2

status: Public on Jan 11 2021

type: SRA

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

country: USA

institute: Vanderbilt University Medical Center

description:
FKBPFV-HCF-1N cells; 3 hours +DMSO
RNA-seq-FKBPFV-HCF-1N-count.txt

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample

molecule: total RNA

organism: Homo sapiens

source_name: Burkitt lymphoma cell line

growth_protocol: Ramos cells were maintained in RPMI 1640 + 10% FBS + penicillin/streptomycin. Cells carrying Cre-ERT2 were additionally maintained in 100 μg/ml hygromycin, and MYC switchable cells (WT, 4A, VP16 HBM) in 150 ng/ml puromycin.

extract_protocol:
For RNA-seq of tumor-derived samples, extraction was performed by Genewiz. Other RNA-seq extractions were performed using TRIzol. For ChIP-seq experiments, cells crosslinked in 1% formaldehyde were subject to sonication, and the resulting sheared chromatin was combined overnight with antibody.
For RNA-seq of tumor-derived or MYC switchable cells (WT, 4A, VP16 HBM), rRNA depletion and library preparation were performed by Genewiz. For RNA-seq of untagged/HCF1N-tagged samples, library preparation was performed by Vanderbilt Technologies for Advanced Genomics (VANTAGE). ChIP-seq libraries were prepared using NEBnext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: See individual samples for relevant treatment protocol

tag: cells

value: Ramos cells

tag: engineered genotype

tag: treatment

value: DMSO for 3 hours


title: dvosA

description: A. nidulans vosA deletion mutant

tag: strain


title: RNA-seq untagged dTAG rep1

description:
untagged, wild-type cells; 3 hours +dTAG-47
RNA-seq-untagged-count.txt

value: 500 nM dTAG-47 for 3 hours


title: RNA-seq untagged DMSO rep3

description:
untagged, wild-type cells; 3 hours +DMSO
RNA-seq-untagged-count.txt


title: d4_P_6

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.3a.
2) Gene read coverages were computed with featureCounts v1.5.2 using ENSEMBL mouse annotation release 92 (GRCm38.92)
3) Differential expression analysis was performed using edgeR v3.22.0 with "y ~ 0 + group + Experiment" design while filtering low read counts less than 2 CPM in at least 5 samples
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

organism: Mus musculus

source_name: Mesenchymal C3H/10T1/2 cells

growth_protocol: Cell were differntiated by targeted over-expression of endogenous Pparγ (transfection with plasmids containing Pparγ-targeted guide RNA) and treated with 5uM Rosiglitazone on day 0 (48 hrs after tranfection) to promote adipogenesis.

extract_protocol:
Cells were lysed with RLT/β-Me and mRNA extracted using Rneasy spin columns (Quiagen) with DNAse treaamnet. mRNA concentrations were determined with nano-drop and RNA quality/integrity assessed using RNA 6000 Nano (Aligent Technology) chips.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: Transfection conditions: EV (Empty Vector plasmid, Control), P (Pparγ gRNA-plasmid only), PY (Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid). All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.

tag: group

tag: transfection

value: Pparγ gRNA-plasmid only

tag: day of differentiation

tag: experiment


title: RNA-seq tumor WT rep3

description:
Tumor-derived Cre-ERT2, MYC-WT cells; 48 hours post 4-OHT treatment
RNA-seq-Tumor-count.txt

value: Tumor-derived MYC-WT

value: 48 hours post 4-OHT treatment


title: hv190

type: RNA

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: Gene expression data from adults

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: miRNA-4_1 chips were scanned at the Cologne Center for Genomics, Cologne, Germany.

data_processing: Pre-processing, normalization, probe summarization, and data quality control were executed in Expression Console Software (Affymetrix). Robust Multi-array Average (RMA)  normalization and DABG probe-level detection were specified. All other parameters were default.

label: biotin

source_name: blood

label_protocol: 100ng total RNA was labeled using standard GeneChip buffers and reagents (Affymetrix)

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood miRNA isolation (QIAGEN) procedure using the QIAcube instrument.

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (approx. 2 hours) while mixing by inversion.

tag: age

tag: gender

value: female

tag: disease state

value: healthy

tag: tissue

value: blood


title: d4_P_5


title: WT

description: A. nidulans Wild Type


title: RNA-seq tumor WT rep2


title: RNA-seq tumor WT rep1


title: RNA-seq untagged DMSO rep1


title: d4_P_4


title: RNA-seq untagged DMSO rep2


title: RNA-seq untagged dTAG rep2


title: VosA-WT

description:
ChIP DNA from wild type spores used as the control sample for the VosA ChIP experiment
VosA_peaks.narrowPeak

library_source: genomic

data_processing:
Raw reads were trimmed using Trimmomatic version 0.36 and the parameters “ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Trimmed reads were mapped to the A. nidulans A4 genome using version 0.7.15 of BWA-MEM and shorter split hits were marked as secondary alignments.
Mapped reads with MAPQ values less than 1, as well as unmapped, secondarily aligned, supplementary, and duplicated reads, were discarded with SAMtools version 1.6.
Mapped reads that survived our filter were pooled and extension sizes were estimated with version 1.15.2 of SPP.
Peaks were called with MACS2 version 2.1.2 using the extension sizes estimated by SPP, a genome size of 2.93e7, and the “--nomodel” parameter.
Genome_build: FungiDB-32_AnidulansFGSCA4
Supplementary_files_format_and_content: Each processed data file is in narrowPeak format (http://www.genome.ucsc.edu/FAQ/FAQformat.html) and contains all peaks called by MACS2

molecule: genomic DNA

extract_protocol:
DNA samples from each strain were extracted using a MAGnify Chromatin Immuno-precipitation System (Invitrogen, USA) according to the manufacturer’s protocol with a modification. Two-day-old conidia from the WT strain, strains containing VosA-FLAG, or VelB-FLAG were cross-linked, washed, homogenized with a Mini-Beadbeater 16 (Biospec, USA), sonicated, and separated with centrifugation. The chromatin extracts were incubated with an anti-FLAG antibody-Dynabead complex. Then, samples were eluted from the beads at 55°C using Proteinase K. Enriched DNA was purified using DNA Purification Magnetic Beads.
Libraries were prepared using a TruSeq ChIP library preparation kit (Illumina, CA). The libraries of all the replicates were sequenced using an Illumina HiSeq 2500 system.


title: VosA-FLAG

description:
ChIP DNA from spores containing FLAG-tagged VosA. Experimental sample for VosA experiment
VosA_peaks.narrowPeak


title: RNA-seq MYC VP16 HBM rep3

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
RNA-seq-MYC-switchable-cells-count.txt

value: Cre-ERT2, MYC-VP16 HBM

value: 20 nM 4-OHT for 24 hours


title: NLH_patient_13 (RNA-seq)

city: Hong Kong

first: Xin-Yuan

last: Guan

address: L10-56, Laboratory Block, LKS Faculty of Medicine

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description:
barcodes.tsv
features.tsv
matrix.mtx

data_processing:
Cell Ranger (version 3.1.0)
The single-cell suspension was converted to uniquely barcoded RNA, TCR and BCR libraries by using the Chromium Single Cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), per manufacturer’s instructions. The libraries were sequenced on a Novaseq 6000, and mapped to the human genome (hg38) using CellRanger (version 3.1.0, 10x Genomics). Gene positions were annotated as per Ensembl build 85 and filtered for biotype (only protein-coding, long intergenic non-coding RNA, antisense, immunoglobulin, T-cell receptor and B-cell receptor).
The raw gene expression matrix generated from each sample were aggregated using CellRanger (version 3.1.0).
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv.gz (barcode-#, where # corresponds to patient_#); features.tsv.gz; matrix.mtx.gz. The files contain aggregated information about unique barcodes, features and gene-cell matrix

source_name: Nasopharyngeal lymphoid hyperplasia

growth_protocol: not applicable

extract_protocol:
Collagenase Type IV+DNAse
The libraries were constructed using the following kits: Chromium Single Cell 5’ Library & Gel Bead Kit, Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, as per manufacturer’s instructions
Single-cell 5' RNA sequencing+ V(D)J sequencing

treatment_protocol: not applicable

value: Nasopharyngeal lymphoid hyperplasia

tag: site

value: Primary


title: VelB-FLAG

description:
ChIP DNA from spores containing FLAG-tagged VelB. Experimental sample for VelB experiment
VelB_peaks.narrowPeak


title: d4_P_3


title: d4_P_2


title: RNA-seq MYC VP16 HBM rep2


title: RNA-seq MYC VP16 HBM rep1


title: VelB-WT

description:
ChIP DNA from wild type spores used as the control sample for the VelB ChIP experiment
VelB_peaks.narrowPeak


title: RNA-seq tumor WT rep4


title: NLH_patient_11, rep2 (RNA-seq)

description: Sequenced from the same tissue as GSM4586338.


title: d0_PY_1

value: Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid


title: NPC_patient_10 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx

source_name: Nasopharyngeal tumor tissue

value: Nasopharyngeal tumor tissue


title: d4_P_1


title: EG1_Etl4_KO_rep3

city: Beijing

first: Xiao

middle: wen

last: Li

state: Beijing

address: Dong Dan San Tiao 5

department: Medical genetics

country: China

institute: Chinese Academy of Medical Sciences Institute of Basic Medical Sciences

description:
Etl4_F1_Rep3
processed data file: gene_counts_matrix2.txt

data_processing:
Basecalls performed using CASAVA.
Reads were aligned with Hisat2 (version 2.1.0) using default settings
Bam to count using featureCounts (Version 1.6.4)
Gene expression analysis was performed using DESeq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: EG1_Etl4_KO_haploid ESCs

extract_protocol:
RNA was harvested using Trizol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype

value: Etl4 KO

tag: cell line

tag: cell type

value: Androgenetic haploid ESCs


title: d2_P_6


title: RNA-seq MYC 4A rep2

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
RNA-seq-MYC-switchable-cells-count.txt

tag: cells

value: Ramos cells

value: Cre-ERT2, MYC-4A


title: EG1_Etl4_KO_rep2

description:
Etl4_F1_Rep2
processed data file: gene_counts_matrix2.txt


title: RNA-seq MYC 4A rep3

tag: engineered genotype


title: NPC_patient_9 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: hv210

description: Gene expression data from adults

tag: treatment


title: d2_P_5

tag: strain


title: EG1_Etl4_KO_rep1

description:
Etl4_F1_Rep1
processed data file: gene_counts_matrix2.txt


title: EG1_rep3

description:
EG1_Rep3
processed data file: gene_counts_matrix2.txt

source_name: EG1_haploid ESCs

value: Wild type


title: RNA-seq MYC 4A rep1


title: NPC_patient_14 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: RNA-seq MYC WT rep3

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
RNA-seq-MYC-switchable-cells-count.txt

value: Cre-ERT2, MYC-WT


title: d2_P_3

tag: group

value: Pparγ gRNA-plasmid only


title: EG1_rep2

description:
EG1_Rep2
processed data file: gene_counts_matrix2.txt


title: NLH_patient_11, rep1 (RNA-seq)

description: Sequenced from the same tissue as GSM4603514.


title: NPC_patient_8 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: NPC_patient_7 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: RNA-seq MYC WT rep1


title: EG1_rep1

description:
EG1_Rep1
processed data file: gene_counts_matrix2.txt


title: d2_P_1

tag: transfection


title: MCF10Ca1h (M3) cells, RNA.NT.sorted.SORE6+

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
Sequencing libraries were generated according to Illumina’s TruSeq® Stranded mRNA Sample Preparation protocol and run on Illumina HiSeq platform PE 125bp cycle
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome Human - hg19 and the annotated transcripts using  STAR 2.5.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: human breast cell lines

growth_protocol: Cells were cultured in DMEM/F12 media supplemented with 5% horse serum.

extract_protocol:
RNA was extracted using TRIzol reagent (Ambion)
RNA was extracted using TRIzol reagent (Ambion).
Sequencing libraries were generated using Illumina TruSeq Stranded Total RNA kit RS-122-2201 protocol.
Sequencing libraries were run on Illumina HiSeq platform with HiSeq 3000/4000 seequencing chemistry for paired-end 125bp cycle runs.

treatment_protocol: Cells were treated with PADI4 inhibitor (GSK484) or control compound (GSK107) for 72 hours. Some samples were FACS sorted for SORE6-/+ populations.

value: MCF10Ca1h (M3)

value: Breast epithelial cells

value: Untreated (UT/NT)

tag: in vivo timepoint

tag: cell sorting

value: FACS sorted

tag: cell population


title: NPC_patient_6 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: OdG_Etl4_KO_2_rep2

description:
Etl4-7a
processed data file: gene_counts_matrix1.txt

source_name: OdG_Etl4_KO_2_haploid ESCs

value: OdG


title: OdG_Etl4_KO_2_rep1

description:
Etl4-7
processed data file: gene_counts_matrix1.txt


title: NPC_patient_5 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: d0_P_4

tag: day of differentiation

tag: experiment


title: OdG_Etl4_KO_1_rep2

description:
Etl4-6a
processed data file: gene_counts_matrix1.txt

source_name: OdG_Etl4_KO_1_haploid ESCs


title: MCF10Ca1h (M3) cells, RNA.NT.sorted.SORE6-


title: d0_P_5


title: d2_P_4


title: NPC_patient_4 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx

tag: tissue


title: MCF10Ca1h (M3) cells, RNA.NT

value: Sham sorted

value: Bulk


title: OdG_Etl4_KO_1_rep1

description:
Etl4-6
processed data file: gene_counts_matrix1.txt


title: RNA-seq MYC WT rep2

value: 20 nM 4-OHT for 24 hours


title: MCF10Ca1h (M3) cells, RNA.GSK484.sorted.SORE6+

value: 72 hrs


title: OdG_rep2

description:
C69-10a
processed data file: gene_counts_matrix1.txt

source_name: OdG_haploid ESCs


title: d2_P_2


title: MCF10Ca1h (M3) cells, RNA.GSK484.sorted.SORE6-


title: d0_P_3


title: NPC_patient_3 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx

value: Nasopharyngeal tumor tissue

tag: site

value: Primary


title: NPC_patient_2 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx


title: NLH_patient_12 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx

value: Nasopharyngeal lymphoid hyperplasia


title: OdG_rep1

description:
C69-10
processed data file: gene_counts_matrix1.txt

tag: strain background

value: Androgenetic haploid ESCs


title: KO_PD1_Neg_LTi_rep2

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

description: RNA-Seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were mapped to the mouse (mm10) genomes with hisat2 (2.1.0) with default settings. We kept one hit if multiple reads were mapped to the same position for each RNA-Seq libraries.
For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
Genome_build: mm10
Supplementary_files_format_and_content: read count: plan text file. Columns from left to right denote ENSEMBL ID, chromosome, start, end,strand,exon length,number of read mapped to exons.

source_name: huPD-1- LTi from Pdcd1hu/-

extract_protocol:
Single cell suspension were obtained from the colon lamina propria of C57BL/6 mice. For sorting huPD-1high LTi and huPD-1- LTi cells, cells were stained with relative antibodies followed by sorting on a BD Aria III cell sorter for  "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1high" and "live Lineage-CD127+KLRG-1-c-Kit+CCR6+huPD-1-" cells.
The sorted LTi were collected in lysis buffer of the SMART-Seq HT Kit (Takara) followed with cDNA synthesis and amplification according to the manufacturer’s protocols. Sequencing libraries were generated using NEB Next Ultra DNA Prep Kit (New England Biolabs), according to the manufacturer’s instruction. Libraries were assessed using the Agilent 2100 Bioanalyzer system and sequenced by paired-end 150 base pair reads using the Illumina NovaSeq platform.

treatment_protocol: Age-matched adult Pdcd1hu/+ mice and Pdcd1hu/- mice were administratedfed with 3% (w/v) DSS  in their drinking water for 6 days, followed with recovery by DSS withdrawal for 1 day.

tag: isolate

value: isolated from colonic lamina propria lymphocytes

tag: in vivo treatment

value: 3% DSS


title: MCF10Ca1h (M3) cells, RNA.CON.sorted.SORE6+

tag: cell line


title: d4_EV_6

value: Empty Vector plasmid


title: d4_EV_5


title: KO_PD1_Hi_LTi_rep2

description: RNA-Seq

source_name: huPD-1high LTi from Pdcd1hu/-


title: Adult - 25 years

city: San Francisco

first: Audrey

last: Parent

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francisco

data_processing:
Data were processed according to the Cell Ranger pipeline (10X Genomics, version 2.0.0, 2.1.1, or 3.0.2).
BAM files were generated with the Cell Ranger software using default parameters.
Gene-barcode matrices were generated from Cell Ranger using default parameteres.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger outputs a .mtx file with the gene (prior to Cell Ranger 3.0) or feature (after Cell Ranger 3.0)-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cell Ranger. The matrix is in market exchange format while the row (gene or feature) and columns (cell barcodes) are provided as TSV files. File formats are documented in the Cell Ranger software manual.

molecule: polyA RNA

source_name: Thymic stroma

extract_protocol:
Thymic tissues placed in RPMI containing 100 μg/ml DNase I were cut into small pieces using scissors. Tissue pieces were transferred into a gentleMACS C tube containing 10 ml of RPMI with DNAse. The gentleMACS Program m_spleen_02 was run three times. Thymic fragments were separated from the thymocytes-rich supernatant by centrifugation. Remaining fragments were transferred back to C tube with fresh RPMI with DNAse before running program m_spleen_01. The supernatant was removed and replaced with 10 ml of digestion medium containing 100 μg/ml DNase I and 100 μg/ml Liberase TM in RPMI. Tubes were moved to a 37°C water bath and fragments were triturated every 5 minutes to mechanically aid digestion. At 30 min, tubes were spun briefly to pellet undigested fragments and the supernatant was discarded. Fresh digestion medium or accumax was added to remaining fragments and the digestion was repeated for another 15-30 minutes until most pieces were digested. Supernatant from this second round of digestion was transferred to a tube containing cold MACS buffer (0.5% BSA, 2 mM EDTA in PBS) to stop the enzymatic digestion. If necessary, a third round of enzymatic digestion was performed on remaining fragments using accumax for an additional 5-10 min. Cells were pooled with the supernatant from the previous round of digestion and were passed through a 40 μm filter (Falcon). Some samples were treated with 2 ml of ACK lysing buffer for 5 min prior to stromal enrichment. For fetal and postnatal tissues, single cells from digested tissue were resuspended in MACS buffer containing 10 μM of the ROCK inhibitor Y-27632. Human CD45 MicroBeads were used to deplete immune cells according to the manufacturer's instructions with the following modification: 5 μL of CD45 MicroBeads per 10e7 total cells were added instead of 20 μL. Stromal cells from adult thymus were enriched using Fluorescence activated cell sorting (FACS). Cells were blocked and stained for 20 min using human-specific antibodies against EPCAM and CD45. After staining, cells were washed and resuspended in FACS buffer containing DAPI. Cells were sorted on BD FACS Aria II. Pre-gating was first done for live cells based the DAPI stain.
Single cells were captured using the 10X Chromium microfluidics system (10X Genomics). The cells were encapsulated and barcoded cDNA libraries were prepared using the single-cell 3' mRNA kit (v2 or v3; 10X Genomics) following the manufacturer's protocol.

tag: cell type

value: Thymic stromal cells

value: Thymic stroma

tag: developmental stage

value: 25 years old


title: d4_EV_4


title: MCF10Ca1h (M3) cells, RNA.CON.sorted.SORE6-

value: MCF10Ca1h (M3)

value: Breast epithelial cells

tag: treatment


title: Postnatal - 10 months_1

description: Same donor as 'Postnatal - 10 months_2'

value: 10 months old


title: MCF10Ca1h (M3) cells, RNA.CON

value: Sham sorted


title: d4_EV_3

tag: strain


title: Postnatal - 10 months_2

description: Same donor as 'Postnatal - 10 months_1'


title: KO_PD1_Hi_LTi_rep1

description: RNA-Seq


title: d0_P_2

tag: group

value: Pparγ gRNA-plasmid only


title: Postnatal - 6 days

value: 6 days old


title: d0_P_1

tag: transfection


title: WT_PD1_Neg_LTi_rep2

description: RNA-Seq

source_name: huPD-1- LTi from Pdcd1hu/+


title: MCF10Ca1h (M3) cells, RNA.GSK484

tag: in vivo timepoint

value: 72 hrs

value: Bulk


title: WT_PD1_Hi_LTi_rep2

description: RNA-Seq

source_name: huPD-1high LTi from Pdcd1hu/+


title: At_whole_root_RNA

city: Santa Fe

first: Andrew

middle: D

last: Farmer

state: NM

address: 2935 Rodeo Park Dr E

institute: NCGR

data_processing:
sNucRNA-seq fastq files processed by cellranger v3.1.0 count pipeline against pre-mrna processed TAIR10/Araport11 reference to produce UMI count matrices
sNucATAC-seq fastq files processed by cellranger-atac v1.2 count pipeline against TAIR10/Araport11/JASPAR2018_CORE_plants_non-redundant_pfms referemce to produce peak calls, count matrices and fragment files
Seurat v3.1.5 integration and clustering of sNucRNA-seq replicates (including co-clustering with WT scRNA-seq from SRX5074330-SRX5074332), cluster-averaged expression calls across sNuc subset within clusters.
Signac v0.2.5/Harmony v1.0 used to integrate sNucATAC-seq replicates, after which Seurat v3.1.5 multimodal integration was performed using RNA-seq clusters as reference with sNucATAC-seq derived gene activity matrix as query. Cluster-averaged fragment counts file derived from Seurat representation.
For bulk RNA-seq, FastQC was used to do the quality control checks on raw sequence data and then the initial 15 bp of the 50-bp reads were trimmed to get rid of adaptors and low quality sequence information. Read mapping to the corresponding reference genome was performed with TopHat (version 2.0.11), embedded with Bowtie2 (version 2.1.0) and SAMtools (version 0.1.19) with default settings (–segment length 17). The counting of mapped reads was performed with Cufflinks2 (version 2.1.1) based on the correction for multiread on (-u -G). A TopHat (version 2.0.11 with embedded Bowtie2 2.1.0) was used for combined region analysis
Genome_build: TAIR10/Araport11
Supplementary_files_format_and_content: tar count matrix files for RNA-seq (10x genomics cellranger filtered counts matrix);
Supplementary_files_format_and_content: tar gzipped h5 and fragment files (10x genomic cellranger-atac fragments, filtered_peak_bc_matrix.h5, singlecell.csv) for ATAC-seq;
Supplementary_files_format_and_content: tsv cluster-averaged UMI/fragment count matrix files for RNA-seq and ATAC-seq integrated across replicates and clustered (available as Series supplementry file)

organism: Arabidopsis thaliana

growth_protocol: plants are grown vertically on MS media plate for 7 days (25C, 16/8hours light-dark cycle) or for 6 days(23C, continous light).

extract_protocol:
Libraries were prepared for sequencing using Ilumina Truseq kit.
For single-nuclei samples, roots were chopped and filtered before nuclei were purified by FACS. For bulk samples, total RNA was extracted from root tips using RNeasy Plant Mini kit (Qiagen). For the whole root sample, root tips were ground directly into the Eppendorf tube by pestle. For the protoplast sample, protoplasts were isolated from root tips and then ground protoplasts by pestle.

tag: genotype

value: 6 days old plant

value: root

tag: molecule subtype

value: mRNA


title: Fetal - 23 wks_2

description: Same donor as 'Fetal - 23 wks_1'

value: 23 weeks gestational age


title: d4_EV_1

tag: day of differentiation


title: At_root_proto_RNA


title: d4_EV_2

tag: experiment


title: NPC_patient_1 (RNA-seq)

description:
barcodes.tsv
features.tsv
matrix.mtx

tag: tissue

value: Nasopharyngeal tumor tissue

value: Primary


title: d2_EV_6

value: Empty Vector plasmid


title: Fetal - 23 wks_1

description: Same donor as 'Fetal - 23 wks_2'

value: Thymic stromal cells

value: Thymic stroma


title: sNucATAC-seq_rep2

extract_protocol:
Chromium Single Cell ATAC Reagent Kits from 10X Genomics
For single-nuclei samples, roots were chopped and filtered before nuclei were purified by FACS. For bulk samples, total RNA was extracted from root tips using RNeasy Plant Mini kit (Qiagen). For the whole root sample, root tips were ground directly into the Eppendorf tube by pestle. For the protoplast sample, protoplasts were isolated from root tips and then ground protoplasts by pestle.

value: 7 days old plant


title: WT_PD1_Neg_LTi_rep1

description: RNA-Seq

value: isolated from colonic lamina propria lymphocytes

value: 3% DSS


title: WT_PD1_Hi_LTi_rep1

description: RNA-Seq


title: sNucRNA-seq_rep5

extract_protocol:
Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry) from 10X Genomics
For single-nuclei samples, roots were chopped and filtered before nuclei were purified by FACS. For bulk samples, total RNA was extracted from root tips using RNeasy Plant Mini kit (Qiagen). For the whole root sample, root tips were ground directly into the Eppendorf tube by pestle. For the protoplast sample, protoplasts were isolated from root tips and then ground protoplasts by pestle.

value: nuclear RNA


title: Fetal - 19 wks

value: 19 weeks gestational age


title: KO_PD1_Neg_LTi_rep1

description: RNA-Seq


title: d2_EV_5


title: d2_EV_4


title: sNucRNA-seq_rep4


title: T47D_TamR_9_DMSO_Tam

city: Pittsburgh

first: Xiaosong

state: Pennsylvania

address: 5150 Centre Ave

department: Pathology

institute: University of Pittsburgh

data_processing:
Quality control test on the sequencing data was done with error rate calculation and a Phred Q20 and Q30 score. All samples passed with error rate (%) < 0.03, Q20 > 97%, and Q30 > 92%.
The preprocessed reads (fastq.gz) were mapped into reference genome (GRCh38.primary_assembly.genome.fa) using Rsubread R package (ver. 2.0.0, Liao et al. 2013).
The transcripts of each sample were assembled based on transcripts per milllion (TPM) mapped reads method. We obtained TPM log2 values and performed quantile normalization for each sample. The sequence read alignment was annotated with gene symbols by using Gencode gene annotation data (gencode.v31.primary_assembly.annotation.gtf).
We extracted 88 of ER target genes (Lin et al. PMID:15345050) from the normalized RNA-seq data and made heatmap to examine the expression pattern changes of ER target genes caused by NLK-specific siRNA and NLK-target drug VX-702.
Genome_build: As reference genome, we downloaded "GRCh38.primary_assembly.genome.fa" file from Ensembl FTP. For gene symbol annotation, we downloaded "gencode.v31.primary_assembly.annotation.gtf" from Gencode FTP.
Supplementary_files_format_and_content: Tab-delimited text files include TPM log2 values for each Sample.

source_name: T47D_TamR human breast cancer cell line

growth_protocol: BT483 cells were cultured in RPMI 1640 (ATCC) with 10%-20% fetal bovine serum and 200 mg/ml L-glutamine (Invitrogen) according to ATCC recommendation. TamR cells were propagated in phenol red-free RPMI 1640, with 5% charcoal-dextran treated fetal bovine serum (CD-FBS, Thermo Fisher Scientific) and 10-7 M Tam. Tamoxifen-resistant cells (TamR) were established by continuous passage of parental cells in the presence of 10-7 M Tam.

extract_protocol:
Total RNA was extracted from cells in individual confluent 10 cm dish, using the standard procedure of Qiagen RNeasy kit. The primary quantitation and degradation or the extracted RNA were checked by nanodrop and agrose gel electrophoresis. The integrity and purity of RNA were examined by Agilent 2100.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
The final libraries were normalized by quantification with LightCycler 480 II (Roche Applied Science, Indianapolis, IN, USA) and qualification with Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: The NLK-specific siRNA#1 (5′-GUCAGUAACAGAUCCAAGA-3’) siRNA#2 (5’-GAGCUGAAUUUGAAGACUA-3’) and control siRNAs (ON-TARGETplus Non-targeting Pool, D-001810-10-50) were purchased from Dharmacon. We also purchased a Sigma version NLK siRNA#1 with the same sequence as the Dharmacon version (5′-GUCAGUAACAGAUCCAAGA-3’) but exhibit more potent inhibition of NLK expression. The siRNAs were transfected using Lipofectamine RNAi MAX Reagent (Invitrogen) according to the manufacturer’s protocol. T47D-TamR cells were generated in Dr. Rachel Schiff’s lab

tag: sirna or drug

value: DMSO and Tamoxifen


title: sNucRNA-seq_rep3


title: d2_EV_2


title: sNucRNA-seq_rep2


title: T47D_TamR_7_DMSO

value: Negative control:DMSO


title: T47D_TamR_8_VX-702

value: NLK-target drug, VX-702


title: d2_EV_3


title: d2_EV_1


title: d0_EV_5


title: sNucRNA-seq_rep1


title: T47D_TamR_4_siCtrl_Tam

value: Control siRNA and Tamoxifen


title: T47D_TamR_3_siNLK_type2

value: NLK-specific siRNA type2


title: d0_EV_4


title: T47D_TamR_2_siNLK_type1

value: NLK-specific siRNA type1


title: d0_EV_3


title: T47D_TamR_1_siCtrl

value: Negative control:control siRNA


title: Liver_Treated_sample_3

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.7.7a with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM
Counts per Million (CPM) values were calculated using edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver cells

extract_protocol:
Total RNA was extracted from the vehicle and bortezomib treated mice livers using TRIzol and purified according to manufacter's instructions.
A modified NEBNext RNA Ultra II directional protocol was used to prepare the libraries for total RNA.

value: Liver

value: bortezomib


title: Liver_Control_sample_2

value: control


title: Liver_Control_sample_1


title: Liver_Control_sample_3


title: sNucATAC-seq_rep1

value: root


title: d0_EV_2

source_name: Mesenchymal C3H/10T1/2 cells

value: Empty Vector plasmid


title: Liver_Treated_sample_2


title: BT483_3_siNLK_type2

source_name: BT483 human breast cancer cell line


title: BT483_4_siCtrl_Tam


title: Liver_Treated_sample_1


title: d0_EV_1


title: MCF10Ca1h cells, sh80-2

hyb_protocol: RNA samples were hybridized to Human Clariom S Gene Chip.

scan_protocol: Data were normalized and background-corrected using SCAN.UPC.

data_processing: RMA Normalization

label: Clariom S Human Array

label_protocol: RNA samples were labeled and hybridized to the Clariom S Human Array (Affymetrix).

growth_protocol: MCF10Ca1h cells were cultured in DMEM/F12 media supplemmented with 5% horse serum.

extract_protocol: Total RNA was extracted using TRIzol reagent (Ambion) and analyzed for quality with the Agilent 2100 Bioanalyzer system.

treatment_protocol: MCF10Ca1h cells were transduced with a lentiviral control shRNA (shCON) or PADI4 knockdown (sh80) and selected with puromycin.

value: MCF10Ca1h human breast cancer cell line

value: PADI4 knockdown


title: MCF10Ca1h cells, sh80-3


title: HumanSpermPacBio

city: Rochester

first: Xin

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

description: Summary.xlsx

data_processing:
LoRDEC (version 0.5.3, parameters -k 17 -s 3 -a 50000) was used to perform error correction on the long reads (LRs) with short reads (SRs) as input.
The corrected LRs were aligned to the mm10 or hg38 reference genome using GMAP (version 2014-12-24, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the mm10 or hg38 reference genome using HISAT2 (version 2.0.4, parameters --ignore-quals --dta --threads 10 --max-intronlen 150000).
Illumina short reads were quantified using Salmon (v0.8.2), and TPM values were summaized in the processed data table. Sperm samples were further normalized to the renilla spikein number.
SpermPacBio1-6 were combined, and TestisPacBio1-5 were combined.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Long reads numbers mapped to each transcript have been summarized into Summary.xlsx table. Transcript TPM values were also summarized in the table.

source_name: sperm

extract_protocol:
Before RNA purification, sperm cells were lysed by 1% SDS and 0.1M DTT, with 10 min incubatin on 37 degree. Sperm RNAs were isolated using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina sequencing uses standard RNAseq library construction protocol.

value: purfied human sperm from semen


title: BT483_2_siNLK_type1


title: RNAseq.MouseSperm.cauda.adult

description: Summary.xlsx

value: cauda sperm

tag: age

value: adult


title: HCT15 shKSR1 Poly Rep3

status: Public on Jan 10 2021

city: Omaha

first: Chaitra

last: Rao

state: NE

address: 505 S 45th St

department: Eppley Institute

institute: University of Nebraska Medical Centre

description: polysomal RNA

data_processing:
The reads were mapped to the Homo sapiens (human) genome assembly GRCh38 (hg38) using STAR v2.7 alignment and --quantMode GeneCounts option in STAR 2.7  to obtain the HTSeq counts per gene.
Gencode v22 was used for the transcript/gene annotations.
Translational efficiency was calculated using the R Bioconductor anota2Seq package
HTSeq counts by first removing genes that did not contain expression values in more than 10% of the samples.
Significant genes were obtained using anota2seqDataSetFromMatrix and anota2seqRun function
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Matrix table withHTSeq gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with anota2Seq output for significant gene and every sample

source_name: Colorectal Cancer Cell line

growth_protocol: DMEM 10% FBS

extract_protocol:
The total RNA and RNA pooled from the polysome fraction (fractions 6-9) was isolated using RNAzol. RNA sequencing libraries were prepared using 500 ng of  RNA using Truseq mRNA protocol kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell Treated with 100 µg/mL cycloheximide prior to extraction in polysome lysis buffer (10 mM HEPES, 100 mM KCL, 5 mM MgCl2, 100 µg/mL cycloheximide, 2 mM DTT, 1% Triton-X100, 2.5 µl RNaseOUT).

tag: condition

value: stable expression of KSR1 shRNA


title: MCF10Ca1h cells, sh80-1


title: HCT15 Con Poly Rep3

description: polysomal RNA

value: stable expression of non-targeting control shRNA


title: HCT15 shKSR1 Total Rep3

description: total RNA


title: MCF10Ca1h cells, shCON-1

value: control shRNA


title: MCF10Ca1h cells, shCON-3


title: HCT116 Con Poly Rep3

description: polysomal RNA


title: HCT15 Con Total Rep3

description: total RNA


title: HCT116 shKSR1 Poly Rep3

description: polysomal RNA


title: HCT116 shKSR1 Total Rep3

description: total RNA


title: HCT15 Con Poly Rep2

description: polysomal RNA


title: MCF10Ca1h cells, shCON-2


title: HCT116 shKSR1 Total Rep2

description: total RNA


title: HCT15 shKSR1 Poly Rep2

description: polysomal RNA


title: HCT116 Con Total Rep3

description: total RNA


title: HCT15 Con Total Rep2

description: total RNA


title: HCT116 Con Poly Rep2

description: polysomal RNA


title: HCT116 shKSR1 Poly Rep2

description: polysomal RNA


title: HCT15 shKSR1 Total Rep2

description: total RNA


title: HCT15 shKSR1 Total Rep1

description: total RNA


title: HCT15 shKSR1 Poly Rep1

description: polysomal RNA


title: HCT116 Con Total Rep2

description: total RNA


title: HCT15 Con Poly Rep1

description: polysomal RNA


title: HCT15 Con Total Rep1

description: total RNA


title: BT483_1_siCtrl


title: HCT116 Con Total Rep1

description: total RNA


title: HCT116 Con Poly Rep1

description: polysomal RNA


title: HCT116 shKSR1 Poly Rep1

description: polysomal RNA


title: HCT116 shKSR1 Total Rep1

description: total RNA


title: Wildtype mouse retina

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

data_processing:
Samples were demultiplexed and fastqs were generated from sequencer data using cellranger mkfastq (1.3.0)
Reads were aligned using cellranger count (1.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger filtered matrix output

source_name: retina

extract_protocol:
Three ANT-treated Glast-CreER animals had their retinas pooled and were dissociated for FACS purification. Live purified cells were then pelleted at 300 g for 10 minutes at 4 şC and resuspended in 0.04% BSA in PBS at a concentration of 2,000 cells per uL.
10x Single Cell 3' v1

value: retina

value: wt control


title: ANT treated mouse retina

description: Samples collected at six weeks post TSA

value: ANT


title: -45del1

city: Milwaukee

first: Sridhar

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
Reads were aligned using STAR to mm9
Aligned reads were analyzed using DEXeq
Genome_build: mm9

source_name: murine ESC

growth_protocol: 200K cells were plated in 6 well plates

extract_protocol:
RNA was extracted using Trizol, processed through the Qiagen RNAeasy Mini Plus Kit
RNA-seq libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: 6 days of ethanol (vehicle) or tamoxifen (4OHT)

tag: genotype/variation

value: -45 SE deleted


title: -45del2


title: wt3

value: wildtype


title: wt1


title: wt2


title: ChIP-Spt5_DMSO_NELF-A-B-RNAi_S2

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Bam files were filtered to MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2 with scores representing number of reads normalized by the size of the library. Final bigwig files were obtained using bigwigcompare tool as ratio of ChIP signal to Input. Scores represent number of reads normalized by the size of the library.
RNA-Seq reads were aligned to dm3 Drosophila genome by TopHat2. Differential transcription was analyzed using сuffdiff (basing on two biological replicas). Summary tables of genes and transcripts expression are built using FPKM parameter (number of reads per thousand base pairs of gene / isoforms per million)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT; for ChIP-Seq reads), dm3 (for RNA-seq reads)
Supplementary_files_format_and_content: bigwig

organism: Drosophila melanogaster

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2-modencode) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine (crosslinking in Drosophila tissues was performed by 0,7% formaldehyde). After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-2000 bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with corresponding dsRNA for 5 days. Induction of 20E-dependent genes was performed by adding 0.3uM 20-hydroxyecdysone (20E) dissolved in DMSO for 1 hour. Control cells were treated with equal amount of DMSO.

tag: treatment with dsrna for 5 days

value: NELF A/B RNAi (dsRNA against NELF-A + dsRNA against NELF-B)

value: Control (DMSO) for 1 hour

tag: chip antibody

value: anti-Spt5 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: ChIP-Spt5_20E_1h_NELF-A-B-RNAi_S2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: ChIP-Spt5_DMSO_mock-RNAi_S2

value: mock RNAi (dsRNA against GFP)


title: WM1341D-control

city: NUTLEY

first: EUN JOON

last: LEE

state: NJ

address: 200 METRO BLVD

department: CDI CENTER

institute: HACKENSACK MERIDIAN

data_processing:
Illumina bcl2fastq was used for basecalling.
The sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh19 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step
Extracting gene hit counts; Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Hit Counts converted to TPM with R script. The TPM was normalized and log transformed.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: melanoma

growth_protocol: Cultured in DMEM supplemented with 10% FBS, 2 mM of L-Glu and 1% penicillin/streptomycine, cultured at 37oC and 5% CO2

extract_protocol:
Cells were harvested and total RNA was extracted 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 stndard Illumina protocols.

treatment_protocol: Stable expression of BMP6

tag: cell type

value: cancer

value: wild type control


title: ChIP-NELF-E_20E-1h_S2

value: no treatment

tag: treatment

value: anti-NELF-E antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: WM983B-control


title: RNA-Seq_20E_1h_S2_Schneider_cells_rep1

description:
RNA-Seq_S2_Schneider_cells_20E_1h_vs_DMSO_genes_fpkm.txt
RNA-Seq_S2_Schneider_cells_20E_1h_vs_DMSO_transcripts_fpkm.txt


title: RNA-Seq_DMSO_S2_Schneider_cells_rep2


title: ChIP-NELF-E_DMSO_S2


title: WM1341D-BMP6

value: BMP6 stable expression


title: RNA-Seq_20E_1h_S2_Schneider_cells_rep2


title: RNA-Seq_DMSO_S2_Schneider_cells_rep1


title: Input_prepupa_0-1h_APF

source_name: Prepupa_0-1h APF (Oregon-Modencode)

value: input chromatin (before precipitation)


title: WM983B-BMP6


title: 1205Lu-control


title: Input_larva_L3_PS1-3

source_name: Larva_L3_PS1-3 (Oregon-Modencode)


title: 1205Lu-BMP6


title: Input_6-8h_embryo

source_name: Embryo_6-8h_AEL (Oregon-Modencode)


title: EnzPos_rep3

city: Salisbury

first: Philip

last: Anderson

state: Maryland

address: 1101 Camden Avenue

institute: Salisbury University

data_processing:
Quality control on the sequenced reads was accomplished using FastQC.
Custom scripts were written to count instances of the Cellecta barcodes in the sequenced reads, and to match them to annotation information.
Normalization was accomplished by edgeR version 3.22.3, by the TMM method.
Log_2 of the counts (with a prior count of 3) was performed by edgeR.
Differential expression was performed separately using the limma-trend (Limma version 3.36.2) and negative binomial (edgeR) methods.
Genome_build: hg18
Supplementary_files_format_and_content: TSV (Tab-separated value) files were exported from R using write.table(). In the TotalCounts.tsv file, each row is one barcode, and contains the unnormalized counts data for each of the eight samples with annotation information. The logCPM.tsv file was used as the basis of differential expression. It contains the counts for all eight samples after log_2 transformation and TMM normalization (performed by edgeR).

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN, Cat.# 56304)
The detailed library construction protocol by Cellecta is found in the RNAi Pooled Lentiviral shRNA Libraries User Manual, section 6.2. Briefly, custom PCR primers are used that specifically bind to the Decipher vector at sequences flanking the shRNA-specific barcode sequence, which had integrated into the genome. A second round of PCR is performed to add Illumina P5 and P7 sequencing primers onto the barcoded amplicons. PCR products were then purified by gel electrophoresis before deep sequencing.
Amplification of Cellecta barcode sequences from gDNA

treatment_protocol: EnzNeg cells were treated with DMSO without enzalutamide, and maintained for six days before genomic DNA was harvested. EnzPos cells were treated with 100 nM enzalutamide in DMSO, and maintained for six days before genomic DNA was harvested. Initial cells were untreated, and maintained for six days before genomic DNA was harvested.

value: Prostate Epithelium-like

value: DMSO +100nM Enzalutamide


title: Input_10-12h_embryo

source_name: Embryo_10-12h_AEL (Oregon-Modencode)


title: Input_2-4h_embryo

source_name: Embryo_2-4h_AEL (Oregon-Modencode)


title: ChIP-Pol-S2P_prepupa_0-1h_APF

value: antibodies against RNA polymerase II CTD repeat (phospho S2) were purchased from Abcam (Ab5095)


title: EnzPos_rep1


title: ChIP-Spt5_20E_1h_mock-RNAi_S2


title: ChIP-Pol-S2P_10-12h_embryo


title: EnzNeg_rep2

value: DMSO


title: ChIP-Pol-S2P_6-8h_embryo


title: ChIP-Pol-S2P_larva_L3_PS1-3


title: ChIP-Pol-S2P_2-4h_embryo


title: ChIP-Rpb3_prepupa_0-1h_APF

value: anti-Rpb3 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: Initial_rep1

value: <no treatment>


title: Initial_rep2


title: ChIP-Rpb3_10-12h_embryo


title: 129-5p miRNA methyl RNA IP sample 3

city: Providence

first: Nikos

last: Tapinos

state: RHODE ISLAND

address: 593 Eddy street

department: Neurosurgery

institute: Brown University

data_processing:
Library strategy: MeRIP-seq
Sequence reads were mapped to the hg19 build of the human genome using gsnap with default parameters, looking for know and novel splice sites with the options -N 1 -s Has_37_67_splicesites
Read with a mapping quality of 20 or greater were summarized at the gene level, by counting all reads mapping to any region of any isoform of a gene, using in-house scripts and information from the refGene.txt file of Refseq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz)
The number of reads mapped to a gene was standardized to Read per Million (RPM), and genes expressing less than 5 RPM in at least two samples were discarded, leaving 12118 genes for analysis
Gene expression analysis was done in R, with the limma package and using the Benjamini-Hochberg method to control the False Discovery Rate
To detect RNA methylation, each exonic region was partition into 10-nucleotide contiguous segements, and the number of reads mapping to each segment in the IP and control samples were determined.  The counts in each windows were analyzed with the Fisher Exact Test in R, using as inputs the number of reads in the MeRIP and control (total) samples and the total number of mapped reads in each sample.  Contiguos segments with p-value < 1e-05 were joined.  Regions of at least 90-nucleotides in lengths are considered methylation events (regions longer than 200 nucleotides were split into 200-nucleotide segments).  All samples had approximately 10,000 methylation events; p-values were adjusted when needed to approximate this number.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text file with raw read counts for the 12118 protein-coding genes use for gene expression analysis, after eliminating genes that did not have at least 3 samples with at least 5 reads
Supplementary_files_format_and_content: Tab-separted text files with the coordinates of methylated peaks for each of the three samples, stem and differentiated (six peak files)

source_name: Glioblastoma

growth_protocol: Patient-derived human glioma stem cells and differentiated cells were cultured as previously described (Galli R, Binda E, Orfanelli U, Cipelletti B, Gritti A, De Vitis S, et al. Isolation and characterization of tumorigenic, stem-like neural precursors from human glioblastoma. Cancer Res. 2004;64(19):7011-21.)

extract_protocol:
For MeRIP-seq we IP methylated RNA using a m6A specific antibody and isolated RNA from the immunoprecipitated fragments. RNA for RNA-seq was isolated with a classic Trizol extraction. For Ribo-seq we performed a sucrose gradient extraction of ribosomes and purification of ribosome-bound RNA. In all instances rRNA was depleted before library construction.
Libraries were constructed according to standard Illumina protocols. All libraries were constructed by Genewiz, the Epigenomic Core at Einstein Medical School and the Genomic Core at Tufts University.

value: brain

value: 129-5p miRNA methyl RNA IP

tag: trasfection

value: 129-5p miRNA transfection - methyl RNA IP


title: ChIP-Rpb3_larva_L3_PS1-3


title: ChIP-Rpb3_6-8h_embryo


title: 143-3p miRNA methyl RNA IP sample 3

value: 143-3p miRNA methyl RNA IP

value: 143-3p miRNA transfection - methyl RNA IP


title: Mock miRNA methyl RNA control total sample 3

value: Mock miRNA methyl RNA control total

value: Scrambled miRNA transfection - methyl RNA total RNA control


title: 129-5p miRNA methyl RNA control total sample 3

value: 129-5p miRNA methyl RNA control total

value: 129-5p miRNA transfection - methyl RNA total RNA control


title: ChIP-Rpb3_2-4h_embryo

value: no treatment


title: ChIP-NELF-A_prepupa_0-1h_APF

value: anti-NELF-A antibodies (Mazina et al (2020) Scientific reports 10 (1), 1-14


title: 143-3p miRNA methyl RNA control total sample 2

value: 143-3p miRNA methyl RNA control total

value: 143-3p miRNA transfection - methyl RNA total RNA control


title: ChIP-NELF-A_larva_L3_PS1-3


title: EnzPos_rep2

value: Prostate Epithelium-like

value: DMSO +100nM Enzalutamide


title: Mock miRNA methyl RNA IP sample 3

value: Mock miRNA methyl RNA IP

value: Scrambled miRNA transfection - methyl RNA IP


title: ChIP-NELF-A_6-8h_embryo


title: EnzNeg_rep3

value: DMSO


title: ChIP-NELF-A_2-4h_embryo


title: ChIP-CBP-Neijre_20E-1h_S2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: anti-CBP/p300/Neijre antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: Adult_Testis

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Testis

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult testis


title: 143-3p miRNA methyl RNA IP sample 2

value: brain

value: 143-3p miRNA methyl RNA IP

value: 143-3p miRNA transfection - methyl RNA IP


title: E01F_PGCLC_1

source_name: Primodrial germ cel-like cells

value: Primodrial germ cell-like


title: DSY127_PGCLC_2


title: ChIP-CBP-Neijre_DMSO_S2

value: Control (DMSO) for 1 hour


title: 143-3p miRNA methyl RNA control total sample 3


title: 129-5p miRNA methyl RNA IP sample 2

value: 129-5p miRNA methyl RNA IP

value: 129-5p miRNA transfection - methyl RNA IP


title: ChIP-NELF-A_10-12h_embryo

value: no treatment

value: anti-NELF-A antibodies (Mazina et al (2020) Scientific reports 10 (1), 1-14


title: No40_PGCLC_2


title: No40_PGCLC_1


title: ChIP-Pol-S5P_DMSO_NELF-A-B-RNAi_S2

value: NELF A/B RNAi (dsRNA against NELF-A + dsRNA against NELF-B)

value: antibodies against RNA polymerase II CTD repeat (phospho S5) were purchased from Abcam (Ab5131)


title: HCT116

city: Shanghai

first: shang

last: yuanyuan

address: 150 Jimo Road, Pudong New Area

institute: Shanghai East Hospital, Tongji University School of Medicine

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping. The software miRDeep2 was used to predict novel miRNA by exploring the secondary structure. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the PossionDis, FDR≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference.
Genome_build: hg38
Supplementary_files_format_and_content: reads count files

source_name: cell line

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
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 adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. 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 110~130 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).

tag: cell line

value: colorectal cancer cells


title: RKO

value: RKO


title: HCT116_Radiation_Resistant

tag: phenotype

value: acquired radioresistant


title: Mock miRNA methyl RNA control total sample 2

value: Mock miRNA methyl RNA control total

value: Scrambled miRNA transfection - methyl RNA total RNA control


title: Input_DMSO_mock-RNAi_S2

value: mock RNAi (dsRNA against GFP)

value: input chromatin (before precipitation)


title: ChIP-Pol-S5P_20E_1h_NELF-A-B-RNAi_S2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: NMiPS

source_name: Induced pluripotent stem cell

growth_protocol: See the citation

treatment_protocol: See the citation

value: pluripotent stem cell


title: ChIP-Pol-S5P_DMSO_mock-RNAi_S2


title: 145-5p miRNA methyl RNA IP sample 1

value: brain

value: 145-5p miRNA methyl RNA IP

tag: tag

value: 145-5p miRNA transfection - methyl RNA IP


title: 145-5p miRNA methyl RNA control total sample 1

value: 145-5p miRNA methyl RNA control total

value: 145-5p miRNA transfection - methyl RNA total RNA control


title: 129-5p miRNA methyl RNA control total sample 2

value: 129-5p miRNA methyl RNA control total

value: 129-5p miRNA transfection - methyl RNA total RNA control


title: RKO_Radiation_Resistant


title: ChIP-Pol-S5P_20E_1h_mock-RNAi_S2

value: antibodies against RNA polymerase II CTD repeat (phospho S5) were purchased from Abcam (Ab5131)


title: DSY127_PGCLC_1

value: Primodrial germ cell-like


title: 143-3p miRNA methyl RNA control total sample 1

value: 143-3p miRNA methyl RNA control total

value: 143-3p miRNA transfection - methyl RNA total RNA control


title: 143-3p miRNA methyl RNA IP sample 1

value: 143-3p miRNA methyl RNA IP

value: 143-3p miRNA transfection - methyl RNA IP


title: ChIP-Pol-S2P_20E_1h_NELF-A-B-RNAi_S2

value: NELF A/B RNAi (dsRNA against NELF-A + dsRNA against NELF-B)

value: antibodies against RNA polymerase II CTD repeat (phospho S2) were purchased from Abcam (Ab5095)


title: Mock miRNA methyl RNA control total sample 1

value: Mock miRNA methyl RNA control total

value: Scrambled miRNA transfection - methyl RNA total RNA control


title: ChIP-Pol-S2P_DMSO_NELF-A-B-RNAi_S2

value: Control (DMSO) for 1 hour


title: Mock miRNA methyl RNA IP sample 1

value: brain

value: Mock miRNA methyl RNA IP

value: Scrambled miRNA transfection - methyl RNA IP


title: Mock miRNA methyl RNA IP sample 2


title: ChIP-Pol-S2P_DMSO_mock-RNAi_S2

value: mock RNAi (dsRNA against GFP)


title: Differentiated Total RNA - Sample 3

description:
gbm3Diff_totalRna
geneExpressionTable.txt

data_processing:
Sequence reads were mapped to the hg19 build of the human genome using gsnap with default parameters, looking for know and novel splice sites with the options -N 1 -s Has_37_67_splicesites
Read with a mapping quality of 20 or greater were summarized at the gene level, by counting all reads mapping to any region of any isoform of a gene, using in-house scripts and information from the refGene.txt file of Refseq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz)
The number of reads mapped to a gene was standardized to Read per Million (RPM), and genes expressing less than 5 RPM in at least two samples were discarded, leaving 12118 genes for analysis
Gene expression analysis was done in R, with the limma package and using the Benjamini-Hochberg method to control the False Discovery Rate
To detect RNA methylation, each exonic region was partition into 10-nucleotide contiguous segements, and the number of reads mapping to each segment in the IP and control samples were determined.  The counts in each windows were analyzed with the Fisher Exact Test in R, using as inputs the number of reads in the MeRIP and control (total) samples and the total number of mapped reads in each sample.  Contiguos segments with p-value < 1e-05 were joined.  Regions of at least 90-nucleotides in lengths are considered methylation events (regions longer than 200 nucleotides were split into 200-nucleotide segments).  All samples had approximately 10,000 methylation events; p-values were adjusted when needed to approximate this number.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text file with raw read counts for the 12118 protein-coding genes use for gene expression analysis, after eliminating genes that did not have at least 3 samples with at least 5 reads
Supplementary_files_format_and_content: Tab-separted text files with the coordinates of methylated peaks for each of the three samples, stem and differentiated (six peak files)

value: Differentiated Total RNA


title: ChIP-Pol-S2P_20E_1h_mock-RNAi_S2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: Dex+E2-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression of HL-1 cells treated with dex and E2 after 6hr.
251486841944_1_3

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: HL-1 cells treated with dex and E2

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced per manufacturer’s protocol.

extract_protocol: RNA was isolated from cells using the RNeasy mini kit from Qiagen. RNA quality was analyzed by gel electrophoresis and quantified using UV-spectrophotometer and Nanodrop techniques. RNA quality was further verified by the NIEHS microarray group using the BioAnalyzer technique.

treatment_protocol: HL-1 cells were cultured in Claycomb Media according to the protocols recommended by Millipore Sigma. Cells were treated with vehicle (PBS), 100 nM Dex, 10 nM E2, or 100nM Dex + 10nM E2.

value: HL-1 cells

tag: gender

value: Female

value: Dexamethasone + estradiol (E2)


title: ChIP-Rpb3_20E_1h_NELF-A-B-RNAi_S2

value: anti-Rpb3 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: E2-4

description:
Gene expression of HL-1 cells treated with E2 after 6hr.
251486841944_1_2

source_name: HL-1 cells treated with E2

value: Estradiol (E2)


title: Dex+E2-4

description:
Gene expression of HL-1 cells treated with dex and E2 after 6hr.
251486841944_1_4


title: Dex+E2-1

description:
Gene expression of HL-1 cells treated with dex and E2 after 6hr.
251486841943_1_3


title: E2-3

description:
Gene expression of HL-1 cells treated with E2 after 6hr.
251486841944_1_1


title: ChIP-Rpb3_DMSO_NELF-A-B-RNAi_S2


title: Differentiated Total RNA - Sample 2

description:
gbm2Diff_totalRna
geneExpressionTable.txt


title: Dex+E2-2

description:
Gene expression of HL-1 cells treated with dex and E2 after 6hr.
251486841943_1_4


title: ChIP-Rpb3_20E_1h_mock-RNAi_S2


title: EnzNeg_rep1

value: Prostate Epithelium-like

value: DMSO


title: E2-2

description:
Gene expression of HL-1 cells treated with E2 after 6hr.
251486841942_1_4


title: E2-1

description:
Gene expression of HL-1 cells treated with E2 after 6hr.
251486841942_1_3


title: SCD_WAT_H3K9me3

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

data_processing:
The sequence quality was assessed using FastQC
Adaptors were trimmed using trim_galore
After the data were cleaned, the DNA sequences were aligned to the reference genome (mm9) using Bowtie2 (v2.4.2), and the reads that mapped to multiple sites were removed.
We then performed model-based analysis of ChIP-seq (MACS2) for enriched-region identification
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: White adipose tissue

extract_protocol:
H3K9me2 and H3K9me3 were used for immunoprecipitation
Libraries were prepared using the KAPA Hyper Prep Kit following the manufacturer’s instructions and sequenced with the Illumina HiSeq X Ten system.

treatment_protocol: Formaldehyde was added to a final concentration of 1% and rotated at room temperature for 8 min. Glycine was added to a final concentration of 125 mM to terminate the cross-linking reaction, and the sample was rotated at room temperature for 10 min

tag: antibody

tag: diet

value: control diet


title: SCD_WAT_H3K9me2


title: Dex-1

description:
Gene expression of HL-1 cells treated with dex after 6hr.
251486841941_1_3

source_name: HL-1 cells treated with dex

value: Dexamethasone


title: SCD_WAT_input


title: Dex-4

description:
Gene expression of HL-1 cells treated with dex after 6hr.
251486841943_1_2


title: Differentiated Polysome-associated RNA - Sample 3

description:
gbm3Diff_polysome
geneExpressionTable.txt

data_processing:
Library strategy: Ribo-seq
Sequence reads were mapped to the hg19 build of the human genome using gsnap with default parameters, looking for know and novel splice sites with the options -N 1 -s Has_37_67_splicesites
Read with a mapping quality of 20 or greater were summarized at the gene level, by counting all reads mapping to any region of any isoform of a gene, using in-house scripts and information from the refGene.txt file of Refseq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz)
The number of reads mapped to a gene was standardized to Read per Million (RPM), and genes expressing less than 5 RPM in at least two samples were discarded, leaving 12118 genes for analysis
Gene expression analysis was done in R, with the limma package and using the Benjamini-Hochberg method to control the False Discovery Rate
To detect RNA methylation, each exonic region was partition into 10-nucleotide contiguous segements, and the number of reads mapping to each segment in the IP and control samples were determined.  The counts in each windows were analyzed with the Fisher Exact Test in R, using as inputs the number of reads in the MeRIP and control (total) samples and the total number of mapped reads in each sample.  Contiguos segments with p-value < 1e-05 were joined.  Regions of at least 90-nucleotides in lengths are considered methylation events (regions longer than 200 nucleotides were split into 200-nucleotide segments).  All samples had approximately 10,000 methylation events; p-values were adjusted when needed to approximate this number.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text file with raw read counts for the 12118 protein-coding genes use for gene expression analysis, after eliminating genes that did not have at least 3 samples with at least 5 reads
Supplementary_files_format_and_content: Tab-separted text files with the coordinates of methylated peaks for each of the three samples, stem and differentiated (six peak files)

value: Differentiated Polysome-associated RNA

tag: fraction

value: Polysome-associated RNA


title: Dex-2

description:
Gene expression of HL-1 cells treated with dex after 6hr.
251486841941_1_4


title: Vehicle-2

description:
Gene expression of HL-1 cells treated with vehicle after 6hr.
251486841941_1_2

source_name: HL-1 cells treated with vehicle

value: Vehicle (PBS)


title: Vehicle-3

description:
Gene expression of HL-1 cells treated with vehicle after 6hr.
251486841942_1_1


title: SCD_BAT_H3K9me3

source_name: Brown adipose tissue


title: SCD_BAT_H3K9me2


title: Dex-3

description:
Gene expression of HL-1 cells treated with dex after 6hr.
251486841943_1_1


title: Vehicle-1

description:
Gene expression of HL-1 cells treated with vehicle after 6hr.
251486841941_1_1


title: Differentiated Total RNA - Sample 1

description:
gbm1Diff_totalRna
geneExpressionTable.txt

tag: tissue

value: brain


title: Vehicle-4

description:
Gene expression of HL-1 cells treated with vehicle after 6hr.
251486841942_1_2


title: HFD_WAT_H3K9me3

value: High-fat feeding


title: SCD_BAT_input


title: Stem Total RNA - Sample 3

description:
gbm3_totalRna
geneExpressionTable.txt

value: Stem Total RNA


title: Differentiated Polysome-associated RNA - Sample 1

description:
gbm1Diff_polysome
geneExpressionTable.txt


title: HFD_BAT_H3K9me3


title: Stem Polysome-associated RNA - Sample 3

description:
gbm3_polysome
geneExpressionTable.txt

value: Stem Polysome-associated RNA


title: HFD_WAT_input


title: Differentiated Polysome-associated RNA - Sample 2

description:
gbm2Diff_polysome
geneExpressionTable.txt


title: ChIP-Rpb3_DMSO_mock-RNAi_S2

source_name: S2 Schneider cells

value: mock RNAi (dsRNA against GFP)

value: Control (DMSO) for 1 hour


title: ChIP-NELF-B_20E_1h_mock-RNAi_S2

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: anti-NELF-B antibodies (obtained for the first time in present study) Were raised in rabbits using NELF-B antigen (150-594 aa)


title: HFD_BAT_input


title: ChIP-NELF-A_20E_1h_NELF-A-B-RNAi_S2

value: NELF A/B RNAi (dsRNA against NELF-A + dsRNA against NELF-B)

value: anti-NELF-A antibodies (Mazina et al (2020) Scientific reports 10 (1), 1-14


title: ChIP-NELF-B_DMSO_mock-RNAi_S2


title: ChIP-NELF-B_DMSO_NELF-A-B-RNAi_S2


title: Stem Total RNA - Sample 1

description:
gbm1_totalRna
geneExpressionTable.txt


title: ChIP-NELF-A_DMSO_NELF-A-B-RNAi_S2


title: 4075

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: Rab22a KO mice with 14-day Angiotensin-II (500ng/kg/min) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GCRmm38/mm10(UCSC)
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: abdominal aorta

extract_protocol:
The abdominal aorta were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with mirVana miRNA Isolation Kit (Cat. AM1560, Ambion, Austin, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: strain

value: abdominal aorta

tag: genotype

value: Rab22a KO

value: Angiotensin-II

tag: group


title: 4059


title: 4060


title: 4062


title: ChIP-NELF-A_20E_1h_mock-RNAi_S2


title: 4061

description: Rab22a KO mice with 14-day Saline treatment

value: Saline


title: HFD_WAT_H3K9me2


title: ChIP-NELF-A_DMSO_mock-RNAi_S2


title: 4085


title: HFD_BAT_H3K9me2


title: 4052


title: Stem Total RNA - Sample 2

description:
gbm2_totalRna
geneExpressionTable.txt


title: Differentiated Methyl RNA IP - Sample 3

value: Differentiated Methyl RNA IP

value: Methyl RNA- Immunoprecipitated


title: 3970


title: D2.2BKO.rep2

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
fastqc
The human transcriptome index was generated by RSEM with bowtie2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded
DESeq2 for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: text file with DESeqNormalized value

source_name: Differentiating cells

growth_protocol: The human embryonic stem cell lines (hESCs, Fy-hES-3) were cultured in feeder-free condition (mTeSR1, Stemcell Technology) medium on Matrigel (354277, Corning). Cells were passaged every 4 to 5 days using EDTA. 10 μM ROCK inhibitor (Y-27632, [1254, TOCRIS bioscience]) was added to the media for 24 hr after each passage.

extract_protocol:
Total RNA was isolated using TRIzol™ Reagent (15596026, Invitrogen) and cDNA libraries were generated using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760L, NEB). The Next Generation Sequencing (NGS) libraries were prepared using KAPA Hyper Prep Kit (KK8505, KAPABIOSYSTEMS). All the NGS libraries were quantified using Equalbit dsDNA HS Assay Kit (EQ111-01, Vazyme) using Qubit™ 4 Fluorometer (Q33226, Invitrogen).
The NGS libraries were subjected to paired-end (PE)150 bp sequencing in Illumina Hiseq XTEN platform at Novogene.

treatment_protocol: The 4i hESCs were cultured on Mitomycin-treated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20 % knockout serum replacement (10828-028 or A3181501, ThermoFisher), 2 mM L-glutamine (35050061, ThermoFisher), 0.1 mM nonessential amino acids (11140050, ThermoFisher), 0.1 mM β-mercaptoethanol (21985023, ThermoFisher), 20 ng/ ml human LIF (7734-LF-500, R&D Systems), 8 ng/ ml bFGF (233-FB-001, R&D Systems), 1 ng/ ml TGF-β1 (100-21, Peprotech), 3 µM CHIR99021 (4423, Tocris Bioscience), 1 µM PD0325901 (4192, Tocris Bioscience), 5 µM SB203580 (1202, Tocris Bioscience), and 5 µM SP600125 (1496, Tocris Bioscience). 4i hESCs were induced for 3 to 5 days, and 10 μM ROCK inhibitor was added for 24 hr after the induction. 4i hESCs were dissociated with TrypLE and plated into ultra-low cell attachment U-bottom 96-well plates (7007, Corning) at a density of 4,000 ~ 5,000 cells eachwell in GK15 medium (GMEM [Life Technologies] with 15 % KSR, 0.1 mM NEAA, 2 mM L-glutamine, 1 mM sodium pyruvate, and 0.1 mM β-mercaptoethanol) containing 300 ng/ ml of BMP4 (314-BP-01M, R&D Systems), 100 ng/ ml SCF (255-SC-001, R&D Systems), 100 ng/ ml LIF (7734-LF-500, R&D Systems), 50 ng/ ml EGF (236-EG-01M, R&D Systems) and 10 μM ROCK inhibitor.

tag: day of reprogramming

value: KDM2B KO


title: D2.2BKO.rep1


title: 4048

description: Rab22a WT mice with 14-day Angiotensin-II (500ng/kg/min) treatment

value: Rab22 WT


title: WT Dendritic cells 5

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Ptbp1_DCs_gene.count.txt.gz
Ptbp1_DCs_filtered_gene.fpkm.txt.gz

data_processing:
Clean reads were aligned the mouse genome sequence using HISAT2
StringTie was used to quantify gene and transcript isoform expression based on the aligned reads.
DEGs were identified by DESeq2 package with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene count and FPKM for each sample

source_name: Mouse Dendritic cells

extract_protocol: Total RNA was extracted using TRIzol(Invitrogen, Cat# 15596026). Library construction and data processing were performed by Novogene (Beijing, China),sequenced with an Illumina HiSeq platform that generate 150 bp paired-end reads.

tag: genotype/variation

value: WT

tag: tissue/cell type

value: Dendritic cells

tag: development stage


title: D2.WT.rep2


title: Differentiated Methyl RNA Control - Sample 2

value: brain

tag: treatment

value: Differentiated Methyl RNA Control

value: Methyl RNA- total RNA control


title: Stem Polysome-associated RNA - Sample 1

description:
gbm1_polysome
geneExpressionTable.txt

value: Stem Polysome-associated RNA

value: Polysome-associated RNA


title: 4046


title: 3987


title: WT Dendritic cells 4


title: WT Dendritic cells 3


title: 3986


title: Differentiated Methyl RNA IP - Sample 2


title: D1.2BKO.rep2


title: Differentiated Methyl RNA Control - Sample 1


title: Differentiated Methyl RNA Control - Sample 3


title: D2.WT.rep1


title: Differentiated Methyl RNA IP - Sample 1


title: 3989


title: Stem Methyl RNA Control Total - Sample 3

value: Stem Methyl RNA Control Total


title: D1.2BKO.rep1


title: Stem Polysome-associated RNA - Sample 2

description:
gbm2_polysome
geneExpressionTable.txt


title: Stem Methyl RNA IP - Sample 3

value: Stem Methyl RNA IP


title: D1.WT.rep2


title: 3994

description: Rab22a WT mice with 14-day Saline treatment

value: abdominal aorta


title: WT Dendritic cells 2


title: WT Dendritic cells 1


title: D1.WT.rep1


title: ChIP-NELF-B_20E_1h_NELF-A-B-RNAi_S2

tag: treatment with dsrna for 5 days

value: NELF A/B RNAi (dsRNA against NELF-A + dsRNA against NELF-B)

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

tag: chip antibody

value: anti-NELF-B antibodies (obtained for the first time in present study) Were raised in rabbits using NELF-B antigen (150-594 aa)


title: Ptbp1 deficiency  Dendritic cells 5

value: Ptbp1 deficient


title: 3971

value: Saline


title: Ptbp1 deficiency  Dendritic cells 4


title: ES.2BKO.rep2

source_name: ESC primed

value: day -4

value: KDM2B KO


title: 4058

value: Rab22a KO


title: Stem Methyl RNA IP - Sample 2

value: Methyl RNA- Immunoprecipitated


title: 4086

value: Rab22 WT


title: ES.WT.rep2

value: WT


title: Ptbp1 deficiency  Dendritic cells 3

value: Dendritic cells


title: Ptbp1 deficiency  Dendritic cells 2


title: 4000


title: Stem Methyl RNA Control Total - Sample 1

value: brain

value: Methyl RNA- total RNA control


title: ES.2BKO.rep1


title: 3988

value: Angiotensin-II


title: Stem Methyl RNA IP - Sample 1

value: Stem Methyl RNA IP


title: Ptbp1 deficiency  Dendritic cells 1


title: ES.WT.rep1


title: Stem Methyl RNA Control Total - Sample 2

value: Stem Methyl RNA Control Total


title: Day20_b

status: Public on Jan 09 2021

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

hyb_protocol: Overnight at 65 deg C in Agilent hybridization buffer

scan_protocol: Slides were scanned on an Agilent scanner immediately after washing

data_processing: Scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters

source_name: HBEC in vitro ALI differentiation_Day 20

label_protocol: Total RNA was labeled with Cy3-CTP

growth_protocol: Primary human bronchial epithelial cells were cultured at air-liquid-interface to generate a fully differentiated airway epithelium.

extract_protocol: Air-liquid-interface cultured human bronchial epithelial cells were harvested and stored in Trizol at -80C until RNA extraction. miRNeasy mini kit (Qiagen) was used for RNA extraction according to the manufacturer’s protocol.

tag: subject id

value: donor b

tag: cell type

value: primary human bronchial epithelial cells (HBECs)

tag: time point

value: Day 20


title: Day22_a

source_name: HBEC in vitro ALI differentiation_Day 22

value: donor a

value: Day 22


title: Day22_b


title: Day18_b

source_name: HBEC in vitro ALI differentiation_Day 18

value: Day 18


title: Day20_a


title: Day18_a


title: Day13_b

source_name: HBEC in vitro ALI differentiation_Day 13

value: Day 13


title: Day15_a

source_name: HBEC in vitro ALI differentiation_Day 15

value: Day 15


title: Day13_a


title: 3996

value: abdominal aorta

value: Saline


title: Day08_b

source_name: HBEC in vitro ALI differentiation_Day 8

value: Day 8


title: Day11_b

source_name: HBEC in vitro ALI differentiation_Day 11

value: Day 11


title: G. diazotrophicus cells, 37 µM FeCl3 R2

city: Seropédica

first: Leonardo

middle: Araujo

last: Terra

state: RJ

address: Rodovia BR-465

country: Brazil

institute: Embrapa Agrobiologia

data_processing:
CLC Genomics Workbench version 7.5.1 program
Reads containing ≤ 20 bp, and those mapping to rRNA 5S, 16S and 23S genes, were all discarded. The following parameters were used: the reads were trimmed for 20 bp, minimum 90% alignment with the reference sequence and 80% identity for inclusion as mapped read and the number of hits equal 1.
The genes were considered expressed if more than three times of coverage was present. They were considered to be differentially expressed genes when the fold change was bigger than 1.2 or smaller than -1.2 and the p-value was smaller than 0.05 by t’test.
Gene ontology analysis was performed using the bioinformatics tool Blast2GO (https://www.blast2go.com/) (70). The genes were function classified by COG (Clusters if Orthologous Groups of proteins, (http://www.ncbi.nlm.nih.gov/COG).
Real-time quantitative (RT-qPCR) was used to validate the transcriptome.
Genome_build: genome of Gluconacetobacter diazotrophicus PAL5  (NCBI accession number NC_010125.1)
Supplementary_files_format_and_content: Tab delimited text files include the reads of each biological sample, RPKM values for each Sample and statistical analysis.

organism: Gluconacetobacter diazotrophicus

source_name: Cultured cells

growth_protocol: PAL5T strain were cultured in 5 ml of modified LGI-P medium at 30°C and 180 rpm for approximately 48 hours. After this period, a pre-inoculum (1.0 × 106 cells) was suspended in 100 µl of saline solution [0.7 % NaCl (w/v)] and inoculated in flasks containing 250 ml of modified LGI-P medium without the addition of FeCl3. The erlenmeyer flask was then incubated at 30°C and 180 rpm until the cell density reached the exponential growth phase (0.6 O.D.600 ml-1) (Optic density at wavelength 600 nm).

extract_protocol:
Total RNA was isolated with Trizol in accordance with the manufacturer’s protocol (Life Technologies) and treated with DNase I (Epicenter) in order to remove genomic DNA contamination. RNA purity was quantified using Qubit (Life Technologies). Seven micrograms of total RNA were used to ribosomal RNA (rRNA) depletion with MICROBExpressTM kit. The efficiency of depletion was evaluated in agarose gel electrophoresis (1%) followed by quantification of the total RNA with Agilent 2100 Bioanalyzer (Agilent).
A total of 500 ng mRNA was used for the contruction of a sequencing library using the standard protocol of the SOLid Total RNAseq Kit (Life Technologies). The libraries were barcoded by using the SOLiD Transcriptome Multiplexing Kit (Life Technologies). The emulsion PCR and sequencing were performed according to Ion One TouchTM 200 Template Kit v2 DL and Ion PITM Sequencing 200 Kit v2 using the standard Life Technologies protocols, respectively. The Ion Proton Semiconductor Sequence (Life) was used to sequence twelve libraries generated from three biological replicates from each independent treatment.

treatment_protocol: Subsequently, cultures were split into aliquots of 25 ml, put into 250 ml flasks and treated with FeCl3 (37 µM) or left untreated. This was done to ensure that all cells would be in the same growth phase for transcriptome sequencing (RNA-seq) analysis. After 30 min of incubation, cells were collected (5,000 rpm, 10 min, 4°C) and stored at -70°C.

value: 37 µM FeCl3


title: Day06_b

source_name: HBEC in vitro ALI differentiation_Day 6

value: Day 6


title: G. diazotrophicus cells, 37 µM FeCl3 R3


title: G. diazotrophicus cells, 0 µM FeCl3 R2

value: 0 µM FeCl3


title: G. diazotrophicus cells, 37 µM FeCl3 R1


title: G. diazotrophicus cells, 0 µM FeCl3 R1


title: Day06_a


title: Day04_b

source_name: HBEC in vitro ALI differentiation_Day 4

value: Day 4


title: G. diazotrophicus cells, 0 µM FeCl3 R3


title: Day04_a


title: Day15_b


title: 100cells_15

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Comma-separated (.csv) file include FPKM values for all the samples in the matrix form

organism: Plasmodium falciparum

source_name: in vitro 3D7 strain culture

growth_protocol: P. falciparum 3D7 strain and subclone was maintained in RPMI 1640 medium (Gibco) supplemented with Albumax I (Gibco) (0.25%), hypoxanthine (Sigma) (0.1 mM), Sodium bicarbonate (Sigma) (2 g/L), and gentamicin (Gibco) (50 μg/L) in 2 % haematocrit at 37 oC on shaker.

extract_protocol:
Single cells were FACS sorted into lysis buffer directly. Total cell lysate was used for reverse transcription and cDNA amplification.
Illumina Nextera XT kit was used for library preparation according to the manufacturer's intructions.

tag: developmental stage

value: blood stage schizonts

value: 3D7 strain


title: 100cells_13


title: 100cells_14


title: dilution_control_48


title: Day08_a

value: primary human bronchial epithelial cells (HBECs)


title: dilution_control_43


title: dilution_control_46


title: dilution_control_44


title: dilution_control_45


title: Day11_a


title: dilution_control_42


title: dilution_control_41


title: dilution_control_39


title: dilution_control_38


title: singlecell_294


title: dilution_control_49


title: dilution_control_40


title: singlecell_295


title: singlecell_293


title: singlecell_292


title: singlecell_286


title: singlecell_290


title: singlecell_287


title: singlecell_288


title: singlecell_289


title: singlecell_291


title: singlecell_280


title: singlecell_282


title: singlecell_283


title: singlecell_284


title: dilution_control_47


title: singlecell_279


title: singlecell_278


title: singlecell_275


title: singlecell_277


title: singlecell_274


title: singlecell_276


title: singlecell_271


title: singlecell_272


title: singlecell_273


title: singlecell_269


title: singlecell_266


title: singlecell_267


title: singlecell_270


title: singlecell_263


title: singlecell_268


title: singlecell_264


title: singlecell_259


title: singlecell_258


title: singlecell_265


title: singlecell_260


title: singlecell_261


title: singlecell_257


title: singlecell_262


title: singlecell_256


title: singlecell_281


title: singlecell_255


title: singlecell_253


title: singlecell_254


title: singlecell_252


title: singlecell_251


title: singlecell_250


title: singlecell_285


title: singlecell_249


title: singlecell_246


title: singlecell_248


title: singlecell_244


title: singlecell_247


title: singlecell_245


title: singlecell_241


title: singlecell_242


title: singlecell_238


title: singlecell_237


title: singlecell_240


title: singlecell_239


title: singlecell_234


title: singlecell_235


title: singlecell_243


title: singlecell_236


title: singlecell_231


title: singlecell_229


title: singlecell_230


title: singlecell_233


title: singlecell_232


title: singlecell_225


title: 100cells_12


title: singlecell_226


title: singlecell_227


title: singlecell_224


title: 100cells_11


title: 100cells_10


title: singlecell_228


title: dilution_control_35


title: dilution_control_34


title: dilution_control_36


title: dilution_control_33


title: dilution_control_37


title: dilution_control_32


title: singlecell_223


title: dilution_control_31


title: singlecell_222


title: singlecell_219


title: singlecell_220


title: singlecell_218


title: dilution_control_30


title: singlecell_217


title: singlecell_216


title: singlecell_214


title: singlecell_215


title: singlecell_210


title: singlecell_213


title: singlecell_212


title: singlecell_211


title: singlecell_208


title: singlecell_207


title: singlecell_205


title: singlecell_204


title: singlecell_209


title: singlecell_203


title: singlecell_206


title: singlecell_202


title: singlecell_201


title: singlecell_198


title: singlecell_221


title: singlecell_197


title: singlecell_200


title: singlecell_195


title: singlecell_196


title: singlecell_194


title: singlecell_190


title: singlecell_193


title: singlecell_188


title: singlecell_192


title: singlecell_191


title: singlecell_189


title: singlecell_184


title: singlecell_187


title: singlecell_199


title: singlecell_175


title: singlecell_186


title: singlecell_185


title: singlecell_170


title: singlecell_167


title: singlecell_171


title: singlecell_164


title: singlecell_183


title: singlecell_182


title: singlecell_181


title: singlecell_158


title: singlecell_180


title: singlecell_157


title: singlecell_155


title: singlecell_179


title: singlecell_156


title: singlecell_178


title: singlecell_154


title: singlecell_177


title: singlecell_174


title: singlecell_176


title: singlecell_163


title: dilution_control_28


title: dilution_control_26


title: singlecell_173


title: singlecell_172


title: dilution_control_22


title: dilution_control_23


title: singlecell_169


title: dilution_control_21


title: dilution_control_20


title: singlecell_168


title: singlecell_161


title: singlecell_160


title: singlecell_150


title: singlecell_149


title: dilution_control_25


title: singlecell_159


title: singlecell_143


title: singlecell_166


title: singlecell_142


title: singlecell_165


title: singlecell_137


title: singlecell_136


title: singlecell_134


title: dilution_control_29


title: singlecell_152


title: singlecell_162


title: dilution_control_27


title: dilution_control_24


title: singlecell_140


title: 100cells_9


title: singlecell_128


title: singlecell_129


title: 100cells_8


title: singlecell_153


title: singlecell_130


title: 100cells_7


title: singlecell_147


title: singlecell_123


title: singlecell_148


title: singlecell_146


title: singlecell_121


title: singlecell_145


title: singlecell_141


title: singlecell_144


title: singlecell_139


title: singlecell_118


title: singlecell_151


title: singlecell_138


title: singlecell_117


title: singlecell_135


title: singlecell_132


title: singlecell_114


title: singlecell_115


title: singlecell_133


title: singlecell_125


title: singlecell_111


title: singlecell_131


title: singlecell_110


title: singlecell_127


title: singlecell_124


title: singlecell_105


title: singlecell_106


title: singlecell_126


title: singlecell_122


title: singlecell_116


title: singlecell_104


title: singlecell_113


title: singlecell_119


title: dilution_control_19


title: singlecell_102


title: singlecell_108


title: singlecell_109


title: singlecell_103


title: singlecell_100


title: singlecell_101


title: singlecell_107


title: singlecell_120


title: dilution_control_16


title: M3

city: Guangzhou

first: Li

middle: Bu

last: Su

address: No. 100, Xianlie Middle Road, Guangzhou, 510070, PR China

institute: Guangdong Institute of Microbiology

data_processing:
SeqPrep  (https://github.com/jstjohn/SeqPrep) used for basecalling
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads  ere separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
To identify DEGs (differential expression genes) between two different samples, the expression  level of each transcript was calculated according to the transcripts per million reads (TPM)  method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) [3] was used to quantify gene abundances
Supplementary_files_format_and_content: Excel file was genarated according to the transcripts per million reads (TPM) method to identify DEGs (differential expression genes) between two different samples

organism: Saccharomyces cerevisiae

growth_protocol: For cultivation, a single colony was picked up from a fresh YPD plate and transferred to a 5 mL YPD medium. After cultured at 200 rpm and 30°C, 1 mL seed culture was inoculated into a 250 mL shake-ﬂask with 50 mL YPD medium, or modified YPD medium (YPM) to an optical density (OD600) of about 0.05 and then incubated at 30 °C for 24 h.

extract_protocol:
Total RNA of different yeast cells was isolated after about 24 h cultivation using the HiPure Yeast RNA Kit (Magen, Guangzhou, China) according to the manufactur-er’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain type

tag: time


title: dilution_control_18