title: IMSA064_EPI_H

description: Human Bronchial Brushings


title: IMSA061_EPI_M

status: Public on Sep 30 2020

type: SRA

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

country: USA

institute: University of Pittsburgh

description: Human Bronchial Brushings

library_source: transcriptomic

data_processing:
Quality control for raw FASTQ files was performed using FastQC, and the lowquality reads and 3’ adapters were trimmed with Trim Galore! (Babraham Bioinformatics, Cambridge, United Kingdom)
The RNA sequence aligner STAR was used to align the trimmed reads to the reference human genome (hg19)
Gene expression was quantified  from mapped genes using featureCounts
Quantified gene expression was normalized using the rlog package from DESeq2
Samples were controlled for batch effect using the COMBAT algorithm
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: Bronchial Epithelial RNA Extraction

extract_protocol:
Frozen RNA samples were purified removing DNA and rRNA with standard procedures.
cDNA libraries were prepared for sequencing using Illumina protocols. (Illumina Document #1000000040499v00 and Illumina Kit #20020596).

tag: tissue

value: lung

tag: cell type

value: Bronchial Epithelial Cells

tag: diagnosis

value: M/M Asthma

tag: steroid

value: no

tag: gender

value: female

tag: batch

tag: age


title: IMSA054_EPI_S

description: Human Bronchial Brushings

value: Severe Asthma

value: yes


title: IMSA049_EPI_H

description: Human Bronchial Brushings

value: Healthy Control


title: IMSA056_EPI_M

description: Human Bronchial Brushings


title: IMSA047_EPI_M

description: Human Bronchial Brushings


title: IMSA058_EPI_M

description: Human Bronchial Brushings

value: male


title: IMSA055_EPI_S

description: Human Bronchial Brushings


title: IMSA053_EPI_M

description: Human Bronchial Brushings


title: IMSA057_EPI_M

description: Human Bronchial Brushings


title: IMSA052_EPI_H

description: Human Bronchial Brushings


title: IMSA046_EPI_M

description: Human Bronchial Brushings


title: IMSA050_EPI_M

description: Human Bronchial Brushings


title: IMSA062_EPI_S

description: Human Bronchial Brushings


title: IMSA059_EPI_S

description: Human Bronchial Brushings


title: IMSA066_EPI_M

description: Human Bronchial Brushings


title: IMSA041_EPI_M

description: Human Bronchial Brushings


title: IMSA045_EPI_S

description: Human Bronchial Brushings


title: IMSA048_EPI_S

description: Human Bronchial Brushings


title: IMSA044_EPI_S

description: Human Bronchial Brushings


title: IMSA039_EPI_S

description: Human Bronchial Brushings


title: IMSA040_EPI_M

description: Human Bronchial Brushings


title: IMSA037_EPI_S

description: Human Bronchial Brushings


title: IMSA038_EPI_M

description: Human Bronchial Brushings


title: IMSA035_EPI_S

description: Human Bronchial Brushings


title: IMSA036_EPI_M

description: Human Bronchial Brushings


title: IMSA028_EPI_M

description: Human Bronchial Brushings


title: IMSA027_EPI_S

description: Human Bronchial Brushings


title: IMSA026_EPI_S

description: Human Bronchial Brushings


title: IMSA023_EPI_M

description: Human Bronchial Brushings


title: IMSA021_EPI_H

description: Human Bronchial Brushings


title: IMSA034_EPI_M

description: Human Bronchial Brushings


title: IMSA008_EPI_M

description: Human Bronchial Brushings


title: IMSA020_EPI_H

description: Human Bronchial Brushings


title: IMSA011_EPI_M

description: Human Bronchial Brushings


title: IMSA031_EPI_S

description: Human Bronchial Brushings


title: IMSA002_EPI_H

description: Human Bronchial Brushings


title: IMSA006_EPI_M

description: Human Bronchial Brushings


title: IMSA007_EPI_S

description: Human Bronchial Brushings


title: IMSA013_EPI_S

description: Human Bronchial Brushings


title: IMSA004_EPI_S

description: Human Bronchial Brushings


title: IMSA010_EPI_M

description: Human Bronchial Brushings

value: n


title: IMSA012_EPI_H

description: Human Bronchial Brushings


title: IMSA022_EPI_M

description: Human Bronchial Brushings


title: IMSA001_EPI_H

description: Human Bronchial Brushings


title: IMSA005_EPI_M

description: Human Bronchial Brushings


title: 07-C6VI2FvectInp

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description: Libraries were generated using a KAPA RNA HyperPrep with RiboErase Kit (Roche) following themanufacturer’s instruction manual

data_processing:
Reads were aligned to the human reference genome (GRCh38.p5) using STAR (version 2.5.1b)
genome was created with a splice junction database based on the Gencode human v24 basic annotation [http://www.gencodegenes.org/]. Sequences that mapped to more than one locus were excluded from downstream analysis, since they cannot be confidently assigned. Other options used include: --outFilterMismatchNmax 3 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 100000.
Uniquely mapped sequences were intersected with composite protein coding gene models from the Gencode human v24 basic annotation using featureCounts (version 1.4.5-p1)
DESeq2 was also used to perform differential gene expression analyses on each cell population separately, identifying genes differentially expressed
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: DESEq2 normalized counts

source_name: Vector, input, U2Os cell line

growth_protocol: U2Os cells (obtained from ATCC) were maintained under standard conditions

extract_protocol:
Libraries were generated using a KAPA RNA HyperPrep with RiboErase Kit (Roche) following the manufacturer’s instruction manual.
All libraries were subjected to flow cell high-output (75 cycles) single-end sequencing on an Illumina NextSeq 500sequencer at the Genomic platform of the Institute of Research in Immunology and Cancer, University of Montréal.

treatment_protocol: transient transfection conditions and generation of stable cell lines are described in SI Appendix

tag: cell line

value: U2Os cell line

tag: antibody

value: input

tag: expression

value: vector


title: 11-C6VI2F4EaCap

source_name: EIF4E-Flag, CapIP, U2Os cell line

value: Cap IP


title: IMSA017_EPI_M

description: Human Bronchial Brushings


title: 02-C5V2FvectaCap

source_name: Vector, CapIP, U2Os cell line


title: 05-C10V2F4EaCap


title: 10-C6VI2F4EInp

source_name: EIF4E-Flag, input, U2Os cell line


title: 20-C6IV2FvectaCap


title: IMSA015_EPI_M

description: Human Bronchial Brushings


title: 08-C6VI2FvectaCap


title: J227_POST

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

data_processing:
For transcriptome analysis, reads were mapped to the EquCab3.0 genome (Ensembl v98) supplemented with the EqHV NZP1 genome (NC_038425) with HISAT2 and quantified with featureCounts including the positive and negative strand of annotation of NZP using default settings. Previous equine transcriptome analysis identified duplicate entries for numerous immunologically relevant genes (CD14, IL7R, etc.) in the EquCab3.0 reference. To recover quantification of genes with duplicate entries (n = 77 genes, which were discarded in initial quantifications due to read multimapping), featureCounts was run a second time on a filtered reference containing only genes with duplicate entries; in this stage, multimapped reads were counted fractionally (each alignment carries 1/x counts where x is the total number of alignments reported for the read) and then collapsed at the gene level by summation  (featureCounts with -m and –fraction explicitly). The resulting counts matrix for genes with duplicate entries was appended to the initial count matrix.  Differential expression was analyzed in R using Limma and Voom. The PRE, ACUTE, SC, FV and POST time points were included in analysis. Horse D was excluded due to persistent infection. Horse B was excluded from liver but not PBMC analysis for technical reasons.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: PBMC Counts matrix. RNA-seq raw read counts for all individual samples are given across genes. Annotations are by Ensembl Gene ID, except for genes found to be multi annotated in which case annotations are by gene names.
Supplementary_files_format_and_content: Liver Counts matrix. RNA-seq raw read counts for all individual samples are given across genes. Annotations are by Ensembl Gene ID, except for genes found to be multi annotated in which case annotations are by gene names.
Supplementary_files_format_and_content: PBMC Voom limma AllTableF. Normalized abundance measurements as determined by voom/limma modelling. For comparison across all time points (F-test), the following is shown: ensembl_gene_id, ensembl_transcript_id, external_gene_name, entrezgene_id, chromosome_name, strand, the normalized expression values for the time points Acute, Seroconversion (SC), Clearance/Falling Viremia (FV), and Post, the average normalized expression values (AveExpr), F, P.Value and adj.P.Val (FDR).
Supplementary_files_format_and_content: Liver Voom limma AllTableF. Normalized abundance measurements as determined by voom/limma modelling. For comparison across all time points (F-test), the following is shown: ensembl_gene_id, ensembl_transcript_id, external_gene_name, entrezgene_id, chromosome_name, strand, the normalized expression values for the time points Acute, Seroconversion (SC), Clearance/Falling Viremia (FV), and Post, the average normalized expression values (AveExpr), F, P.Value and adj.P.Val (FDR).

organism: Equus caballus

source_name: Liver

extract_protocol:
Liver biopsies (~10 mg) fixed in RNA later were transferred into a MagNA Lyser Green Beads tube containing 1 mL cold TRIzol. Liver tissue was homogenized using a MagNA Lyser instrument (Roche) at 6500 rpm for 100 s with continuous cooling on ice every 20 s. PBMCs were directly lysed in TRIzol Reagent (Thermo Fisher Scientific). After addition of chloroform and centrifugation, the aqueous phase was mixed with 450 μL anhydrous ethanol and transferred to an RNA Clean & Concentrator-5 column (Zymo Research) for downstream RNA purification and concentration. The integrity of extracted RNA was analyzed on a 2100 bioanalyzer instrument using an RNA 6000 nano assay kit (Agilent Technologies).
The standard Illumina TrueSeq stranded mRNA library preparation protocol was followed for PBMC mRNA library preparation, starting from 500 ng input RNA. For the liver samples, total RNA-Seq was prioritized over poly(A) selection in order to recover viral reads. Depletion of ribosomal RNA from 500 ng input RNA was achieved using the Ribo-off rRNA depletion kit (Vazyme) for which horse rRNA removal has been validated. Following purification of rRNA-depleted total RNA using VAHTS RNA clean beads (Vazyme), the RNA was eluted into elution buffer ELB (Illumina) for subsequent TrueSeq stranded mRNA library preparation, starting from the mRNA fragmentation step. Quality of DNA libraries was checked using a 2100 bioanalyzer instrument. The Qubit dsDNA High-Sensitivity Assay Kit (Thermo Fisher Scientific) was used to quantify DNA libraries in order to pool these in equimolar concentrations prior to denaturation. Pooled libraries were loaded on a NextSeq 500/550 v2.5 75 cycle flow-cell, and sequencing performed on a NextSeq benchtop sequencer (Illumina) at the Department of Clinical Microbiology (Hvidovre Hospital, Copenhagen). Data derived from two (PBMCs) or three (liver) independent deep-sequencing runs were pooled to ensure sufficient depth of sequencing coverage.

treatment_protocol: PBMCs were prepared by Ficoll density gradient and lysed in Trizol. Liver biopsies were in RNAlater.

value: Liver

tag: time point

value: POST

tag: horse id

value: J


title: J151_FV

value: FV


title: 23-C6IV2F4EaCap


title: B95_FV

value: B


title: 19-C6IV2FvectInp


title: J97_PRE

value: PRE


title: B148_POST


title: B55_ACUTE

value: ACUTE


title: B45_PRE


title: 22-C6IV2F4EInp


title: 04-C10V2F4EInp


title: D46_ACUTE

value: D


title: D108_SC

value: SC


title: 01-C5V2FvectInp


title: D9_PRE


title: B85_SC


title: N76_SC

value: N


title: D69_FV


title: N99_FV


title: N45_ACUTE


title: N8_PRE


title: J132_ACUTE


title: P35_ACUTE

value: P


title: P126_POST


title: P16_PRE


title: P67_SC


title: P83_FV


title: D152_FV


title: A86_FV

value: A


title: A143_CHAL

value: CHAL


title: R8_PRE

value: R


title: R55_SC


title: N139_POST


title: R24_ACUTE


title: A14_PRE


title: A68_SC


title: A123_POST


title: J221_POST

molecule: polyA RNA

source_name: PBMCs

value: PBMCs


title: J92_PRE


title: B143_POST


title: J139_SC


title: J146_FV


title: J128_ACUTE


title: P144_CHAL


title: B60_ACUTE


title: D102_SC


title: B92_FV


title: D64_FV


title: R149_CHAL


title: R118_POST


title: B40_PRE


title: A31_ACUTE


title: N155_CHAL


title: D147_FV


title: B81_SC


title: N132_POST


title: N94_FV


title: P130_POST


title: N49_ACUTE


title: N24_PRE


title: D25_PRE


title: P78_FV


title: R123_POST


title: R144_CHAL


title: R50_SC


title: R2_PRE


title: P12_PRE


title: R67_FV


title: P39_ACUTE


title: A64_SC


title: A138_CHAL


title: D50_ACUTE


title: N80_SC


title: A36_ACUTE


title: R29_ACUTE


title: A128_POST


title: P139_CHAL


title: A10_PRE


title: MAL.P_1

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

data_processing:
The sample replicates were split into 8 Hiseq 2500 sequencing lanes and for each replicate, the lanes were merged into a single count matrix using Cell Ranger v3.0 (10X Genomics). Further, the resultant counts matrices for each replicate were processed using an inhouse single-cell RNA-seq pipeline that uses Seurat v 3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.0 and Integrated matrix file is generated by integrating the samples from healthy controls and Malaria patients using SeuratV3.0

source_name: Malaria_Patient_peripheral blood B cells

growth_protocol: Cell culture protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were isolated with the EasySep  Human B cell isolation kit on a RoboSep platform

extract_protocol:
Cells were encapsulated in droplets using the Chromium Controller (10X Genomics). Reverse transcription and cDNA amplification were performed using the Chromium Single Cell 3’ kit (10X Genomics). All steps were done according to manufacturer’s instructions. 100 ng of cDNA (25% of generated cDNA) was used as input for library preparation.
Libraries were sequenced using the Illumina Hiseq3000 platform 8 lanes of sequencing at 26bp-8bp-98bp according to 10X Genomics sequencing recommendations.

tag: subject status

value: adult living in Malaria-endemic Mali

tag: subject id

value: Patient 1

value: 30 years

tag: Sex

value: Female

value: Blood

value: Peripheral mononuclear blood cells (PBMCs)


title: P60_SC


title: HC_3

source_name: healthy_peripheral blood B cells

value: healthy control adult from US

value: control 3

value: 32 years


title: MAL.P_3

value: Patient 3

value: 27 years


title: HC_2

value: control 2

value: 29 years


title: AC16Spiked_37d_N3_tmaphg19dm6

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

description: Quantseq

data_processing:
Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19 or, for spiked in samples, to a combined hg19 and dm6 genome build.
Mapped reads were narrowed to their 3’ most nucleotide and converted to bigwig files for positive and negative strands
Genome_build: hg19 or combined hg19 and dm6
Supplementary_files_format_and_content: bigwig files of reads narrowed to their 3’ most nucleotide for positive and negative strands. Full length bigwig files are not narrowed but are normalised to counts per million aligned counts (CPM).

organism:
Drosophila melanogaster
Homo sapiens

source_name: AC16 and S2

growth_protocol: The AC16 cardiomyocyte cell line is derived from fusion of primary cells from human ventricular tissues with SV40-transformed fibroblasts (Davidson et al., 2005). AC16 cells were cultured in Dulbecco’s Modified Eagle’s Medium: Nutrient Mixture F-12 (DMEM/F-12) containing 10 % (v/v) Foetal Bovine Serum (FBS), 2.5 mM L-Glutamine and 1 % Penicillin/Streptomycin solution. The U2OS osteosarcoma cells were cultured in DMEM containing 10 % (v/v) FBS, 2.5 mM L-Glutamine 1 % Penicillin/Streptomycin solution

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Neve et al., 2015). For spiked in samples, cells were spiked with a known ratio of D. melanogaster S2 cells prior to subcellular fractionation.
The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen). Full length RNA libraries were generated using the using the Ion Total RNA-seq Kit v2 (ThermoFisher). For this full-length RNA-seq polyadenylated RNAs were first purified from total RNA from each fraction using the NEBNext Poly(A) mRNA Isolation Module.

treatment_protocol: Cells were cultured in a 37°C incubator with 5 % CO2 to 80-90 % confluency before harvesting, passaging or transfer to incubators set at 8°C, 18°C or 28°C (also with 5 % CO2) for the temperature exposure conditions indicated

value: AC16 and S2

tag: subcellular fraction

value: Nuclear

tag: temperature treatment

tag: spike

value: D. melanogaster S2 cells


title: Su.86.86 siJAG1 GF200 002

type: protein

city: Shanghai

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

country: China

institute: Fudan University Shanghai Cancer Center

description: Human Antibody Arrays 507 (L-507, Raybiotech)

hyb_protocol: The array membrans were then incubated with diluted biotin-conjugated antibodies at room temperature for 2 h and then reacted with Cy3-conjugated streptavidin

scan_protocol: The array membrans were scanned by GenePix 4000B Microarray Scanner (Axon Instruments Inc)

data_processing: Quantitative array analysis was performed using GenePix Pro 5.0 Software (Axon Instruments Inc). To obtain relative expression, signal intensity was subtracted for negative controls and normalized to internal positive.

molecule: protein

source_name: Human pancreatic cancer cell line

label_protocol: The array membrans were reacted with Cy3-conjugated streptavidin

growth_protocol: Su.86.86 cells were  grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 ?g/mL each of penicillin and streptomycin at 37°C with 5% CO2 in a humidified atmosphere.

extract_protocol: The array membrans were blocked, incubated with 100 ?L of conditioned medium at room temperature for 2h.

treatment_protocol: Su.86.86 cells were transfected with siNC or siJAG1, and 48h later, the conditioned media were harvested and subjected to human cytokine array.

tag: cell type

value: Human pancreatic cancer cell line


title: Su.86.86 siNC GF200 001


title: AC16Spiked_37d_N4_tmaphg19dm6

description: Quantseq


title: AC16Spiked_37d_C4_tmaphg19dm6

description: Quantseq

value: Cytoplasmic


title: A92_FV

tag: tissue

value: PBMCs

value: FV

value: A


title: HC_1

value: control 1

value: 40 years

value: Female

value: Blood


title: AC16Spiked_37d_C2_tmaphg19dm6

description: Quantseq


title: AC16Spiked_37d_N1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_37d_N2_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h_C2_tmaphg19dm6

description: Quantseq

value: 18°C for 24 h


title: AC16Spiked_18d24h_C3_tmaphg19dm6

description: Quantseq


title: MAL.P_2

value: adult living in Malaria-endemic Mali

value: Patient 2

value: 24 years

value: Peripheral mononuclear blood cells (PBMCs)


title: AC16Spiked_18d24h_N4_tmaphg19dm6

description: Quantseq

value: AC16 and S2


title: AC16Spiked_18d24h37d2h_N4_tmaphg19dm6

description: Quantseq

value: Nuclear

value: 18°C for 24 h, then 37°C for 2 h


title: AC16Spiked_18d24h_C4_tmaphg19dm6

description: Quantseq

value: D. melanogaster S2 cells


title: AC16Spiked_18d24h_N3_tmaphg19dm6

description: Quantseq


title: AC16Spiked_37d_C3_tmaphg19dm6

description: Quantseq

value: Cytoplasmic


title: AC16Spiked_18d24h_C1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h37d2h_C2_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h37d2h_N2_tmaphg19dm6

description: Quantseq


title: HIV_Patient_3_scRNA-seq

data_processing:
The sample replicates were split into 8 Hiseq 2500 sequencing anes and for each replicate, the lanes were merged into a single count matrix using Cell Ranger v4.0 (10X Genomics). Further, the resultant counts matrices for each replicate were processed using an inhouse single-cell RNA-seq pipeline that uses Seurat v 3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: CSV files are generated from CellrangerV4.0 and Integrated matrix file is generated by integrating the samples from healthy controls and HIV patients using SeuratV3.0

source_name: Peripheral mononuclear blood cells (PBMCs)

growth_protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were isolated with the EasySep  Human B cell isolation kit on a RoboSep platform

value: Male


title: AC16Spiked_18d24h37d2h_C4_tmaphg19dm6

description: Quantseq


title: AC16Spiked_37d_C1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h37d2h_N1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h37d2h_C1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h37d2h_N3_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h_N1_tmaphg19dm6

description: Quantseq


title: AC16Spiked_18d24h_N2_tmaphg19dm6

description: Quantseq


title: HIV_Patient_2_scRNA-seq


title: HIV_Patient_1_scRNA-seq


title: U87MG TP53 KO c5.12 rep 1

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
rDNA and low quality read filtering: MOIRAI pipeline (Hasegawa et al. 2014)
genome alignment: BWA version 0.5.9 (r16), parameters outlined in the manuscript
read clustering by overlapping with FANTOM5 robust promoter set
mapping to the nearest GENCODE v27 annotations within 500 bp
merging of CAGE clusters within 20bp of each other
Genome_build: hg38
Supplementary_files_format_and_content: bed

growth_protocol: U87MG cells were grown in high glucose DMEM with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 C with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen).
CAGE libraries were prepared following the nAnT-iCAGE protocol (Murata et al, 2014). 5 μg of total RNA was reverse transcribed, and the resulting cDNA was biotinylated and cap trapped to capture their 5' ends. Sequencing was performed on illumina HiSeq 2500 (50 nt, single read).

tag: tp53 mutation

value: mutated TP53 clone 5.12


title: U87MG TP53 KO c5.9 rep 3

value: mutated TP53 clone 5.9


title: U87MG TP53 KO c5.12 rep 3


title: U87MG TP53 KO c5.5 rep 2

value: mutated TP53 clone 5.5


title: U87MG TP53 KO c5.11 rep 1

value: mutated TP53 clone 5.11


title: U87MG TP53 KO c5.11 rep 2


title: U87MG TP53 KO c5.11 rep 3


title: U87MG TP53 KO c5.12 rep 2


title: U87MG TP53 KO c5.9 rep 2


title: AC16Spiked_18d24h37d2h_C3_tmaphg19dm6

description: Quantseq


title: U87MG TP53 KO c5.5 rep 3


title: U87MG TP53 KO c5.5 rep 1


title: U87MG TP53 KO c4.8 rep 2

value: mutated TP53 clone 4.8


title: U87MG TP53 KO c4.8 rep 3


title: U87MG TP53 KO c4.2 rep 3

value: mutated TP53 clone 4.2


title: U87MG TP53 KO c3.4 rep 3

value: mutated TP53 clone 3.4


title: OE_Rep2

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 16nt-35nt filtered and were analyzed.
Supplementary_files_format_and_content: Text file containing 16nt-35nt long unique reads and their raw abundance after removal of adapter.

organism: Oryza sativa Indica Group

source_name: mature panicle

extract_protocol:
Total RNA mature panicle before anthesis (Stage 12) of both wild-type, over-expression and transgenic knock-down lines of AGO17 were extracted using Trizol (Invitrogen) reagent.
Size fractionation

tag: cultivar

value: Pusa Basmati 1 (PB1)

value: mature panicle


title: WT_Rep2


title: KD_Rep1


title: KD_Rep2


title: U87MG TP53 KO c4.2 rep 1


title: U87MG wild type rep 3

value: wild type TP53


title: U87MG TP53 KO c3.4 rep 1


title: PB-1_Seedling

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
small RNAs matching rRNA and tRNA are filtered out
20-21nt small RNA reads were size selected
Supplementary_files_format_and_content: Text files including read sequence and its count for each sample.

source_name: Four weeks old seedlings

extract_protocol:
Total RNA from three different tissues, 4-week old seedling and, flagleaf and panicle (equal concentration of flagleaf RNA and panicle RNA were mixed) of two rice species were extracted using Trizol (Invitrogen) reagent.
Degradome cDNA libraries were construction according to J. Zhai et al., 2014, Methods, 67 (84–90) protocol with slight modifications.

tag: variety

value: Pusa Basmati 1 (PB-1)

value: Four weeks old seedlings


title: U87MG TP53 KO c3.4 rep 2


title: WT_Rep1


title: U87MG wild type rep 2


title: PB-1_Flagleaf_Panicle

source_name: Flagleaf and Panicle

value: Flagleaf and Panicle


title: U87MG TP53 KO c4.8 rep 1


title: U87MG TP53 KO c5.9 rep 1


title: U87MG TP53 KO c4.2 rep 2


title: OE_Rep1


title: ScRe56

city: Westmead

first: Lawrence

last: Ong

state: NSW

address: 176 Hawkesbury Road

country: Australia

institute: Westmead Institute for Medical Research

library_source: genomic

data_processing:
QC of raw sequence reads was performed using FastQC v0.10.1
Adapter trimming was done using Trimmomatic v0.36 using ILLUMINACLIP option with seed mismatches = 2, palindrome clip threshold = 30, simple clip threshold = 3 and MAXINFO option with target length = 40 and strictness = 0.5
Alignment was peformed with wildcard alignment tool (WALT)
Methylation calls and CpG island methylation analysis was performed using Methpipe
Genome_build: hg19
Supplementary_files_format_and_content: .meth files were generated using Methpipe. The files contain average methylation over discrete hg19 annotated CpG islands in tab delimited text format.

molecule: genomic DNA

source_name: peripheral blood

growth_protocol: not applicable

extract_protocol:
DNA was extracted from isolated cells using the QIAamp DNA micro kit as per manufacturer's instructions
Next generation sequencing libraries were prepared using gel-free modified reduced bisulfite sequencing as previously described (Boyle et al, Genome Biol, 2012, 13(10): R92). Briefly, 100ng of input DNA was digested with MspI prior to end repair and A-tailing. Methylated Illumina indexes were then ligated to these fragments prior to bisulfite conversion. Bisulfite converted libraries were then subjected to PCR and SPRI bead cleanup.

treatment_protocol: not applicable

tag: subset


title: PrGa56

value: Female


title: ScRe14


title: StSc14


title: StSc56


title: PrGa14


title: ScRe34


title: StSc34


title: Mouse treated Adhatoda Vasica 260mg/kg (AV-D4)- 3

type: RNA

city: Delhi

first: Mitali

last: Mukerji

address: Mathura Road

institute: CSIR-IGIB

hyb_protocol: 5.2 µg of fragmented and labelled ss cDNA were hybridized on Affymetrix MTA 1.0 Cartridge arrays for 16hrs at 45°C at 60rpm in Affymetrix hybridization oven. Arraya were stained and washed in the Affymetrix Fluidics Station 450

scan_protocol: The stained chips were then scanned using GeneChip™ Scanner 3000

data_processing: CEL files were processed using Oligo package of Bioconductior. The intensity values were background corrected, normalised and summarised based on probe level information using Robust multi-array (RMA) normalization.

label: Biotin

organism: Mus musculus

source_name: lung

label_protocol: Fragmented and biotin labelled Second cycle single stranded cDNA were prepared from 250ng total RNA following the manufacturers protocol (GeneChip WT plus reagent kit user manual)

extract_protocol: Total RNA was extracted using Trizol according to manufacturers instructions

treatment_protocol: BALB/c mice were treated with mentioned doses of  aqeuous extract of Adhatoda Vasica (distilled water was used as vehicle)  for four consecutive days.

tag: strain

value: BALB/c

tag: treatment

value: Adhatoda Vasica 260mg/kg

value: lung


title: PrGa34


title: Mouse treated Adhatoda Vasica 130mg/kg (AV-D2)- 4

value: Adhatoda Vasica 130mg/kg


title: Mouse treated Adhatoda Vasica 260mg/kg (AV-D4)- 4


title: Mouse treated Adhatoda Vasica 130mg/kg (AV-D2)- 5


title: Mouse treated Adhatoda Vasica 130mg/kg (AV-D2)- 3


title: Mouse treated Adhatoda Vasica 0.130mg/kg (AV-D0)- 3

value: Adhatoda Vasica 0.130mg/kg


title: Mouse treated Adhatoda Vasica 260mg/kg (AV-D4)- 2


title: Vehicle (distilled water) treated Mouse-4

value: Vehicle treated


title: Vehicle (distilled water) treated Mouse-1


title: R72_FV

value: Liver

value: FV

value: R


title: Vehicle (distilled water) treated Mouse-2


title: Mouse treated Adhatoda Vasica 130mg/kg (AV-D2)- 1


title: Mouse treated Adhatoda Vasica 0.130mg/kg (AV-D0)- 4


title: NiFe56


title: Mouse treated Adhatoda Vasica 130mg/kg (AV-D2)- 2


title: Mouse treated Adhatoda Vasica 0.130mg/kg (AV-D0)- 2


title: NiFe34


title: JuDj56


title: NiFe14


title: Mouse treated Adhatoda Vasica 260mg/kg (AV-D4)- 1


title: Mouse treated Adhatoda Vasica 0.130mg/kg (AV-D0)- 1


title: JiWu14


title: JuDj14


title: GrPa56

value: Male


title: GrPa34


title: JuDj34


title: JiWu34


title: GrPa14


title: DeDe56


title: JiWu56


title: EuLe34


title: Vehicle (distilled water) treated Mouse-3


title: EuLe56


title: DeDe34


title: DaBo56


title: CeLi56


title: U87MG wild type rep 1


title: DaBo14


title: DaBo34


title: DeDe14


title: CeLi34


title: CeLi14


title: RJ052C

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg38) using HISAT2 version 2.1.0   with the default options with a TopHat transcript index built from Ensembl_GRCh38.
Count files of the aligned sequencing reads were generated by the featurecount
Genome_build: hg38
Supplementary_files_format_and_content: count file

source_name: human colorectal cancer tissue

extract_protocol:
Total RNA of colorectal tissues was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colorectal cancer tissue

tag: passage


title: RJ050C


title: RJ046C


title: RJ051C


title: RJ049C


title: RJ053C


title: RJ048C


title: RJ045C


title: RJ044C


title: RJ037C


title: RJ034C


title: RJ042C


title: RJ043C


title: RJ028C


title: RJ040C


title: RJ039C


title: RJ030C


title: RJ033C


title: RJ029C


title: RJ036C


title: RJ032C


title: RJ025C


title: RJ038C


title: RJ031C


title: RJ019C


title: RJ015C


title: RJ027C


title: RJ026C


title: RJ016C


title: RJ047C


title: RJ012C


title: RJ041C


title: RJ023C


title: RJ020C


title: RJ014C


title: RJ013C


title: RJ018C


title: RJ011C


title: RJ010C


title: RJ017C


title: RJ021C


title: RJ007C


title: RJ009C


title: RJ006C


title: RJ024C


title: RJ003C


title: RJ008C


title: RJ004C


title: RJ002C


title: RJ001C


title: MDA231ERb_E2+TNFa_RNAPIIpS2

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: E3-MDA_4-pol-24.FCHWYW5BBXX_L2_IGGTTGGAC

data_processing:
Raw sequencing reads were analyzed using the HiChIP pipeline
Paired-end reads were mapped to the human reference genome (hg38) by Burrows-Wheeler Alignment (BWA) with default settings, and only pairs with at least one of the ends being uniquely mapped were retained for further analysis
Alignments were position sorted and duplicates were removed using the Picard tools
For all samples except KA41-48, peaks were called using the MACS2 algorithm  at FDR ≤ 1%. For samples KA41-KA48 K27me3, peaks were called using SICER.
Genome_build: Hg38
Supplementary_files_format_and_content: Peak files from MACS2 in BED format, and from SICER in TSV format

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231-ERβ cells were seeded in 10cm dishes in charcoal-stripped serum-containing medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Antibodies include: H3K27me3 (Abcam ab 6002), H3K27ac (Abcam ab 4729), NFκB (Cell signaling 8242), RNA Pol II phospho Ser2 (Bethyl, A300-654A)
ChIP-seq libraries were prepared from immunoprecipitated chromatin solutions and input DNA using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI).

treatment_protocol: Cells were treated with doxycyline to induce ERβ expression followed by vehicle or E2 at the time of seeding. Media was refreshed after 3 days. After a total of 5 days, 20ng/ml TNFα was spiked in for 30 minutes. Cells were then harvested via ChIP protocol.

tag: cell line

tag: antibody

value: RNA Pol II phospho Ser2


title: MDA231ERb_E2_RNAPIIpS2

description: E3-MDA_2-pol-22.FCHWYW5BBXX_L2_ITGATACGT


title: MDA231ERb_TNFa_RNAPIIpS2

description: E3-MDA_3-pol-23.FCHWYW5BBXX_L2_IGTGCTACC

value: TNFα


title: MDA231ERb_E2+TNFa_NFkB_rep1

value: NFκB


title: P25_S10

first: Ken

last: Dower

state: MA

address: 1 Portland Street

department: Inflammation & Immunology

institute: Pfizer

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: hg19; mm10; hg19_mm10
Supplementary_files_format_and_content: human or mouse UMI-collapsed transcripts, gene counts

source_name: Transcriptome of single cells

extract_protocol:
Seq-Well, 10x Chrominum V3, Smart-Seq2
Illumina Nextera XT

tag: genome build

tag: sample type

value: Human Peripheral Blood Mononuclear Cells

tag: condition

value: Healthy Primary PBMCs


title: MDA231ERb_TNFa_NFkB_rep2


title: MDA231ERb_E2+TNFa_NFkB_rep2


title: MDA231ERb_TNFa_NFkB_rep1


title: P24_S9


title: MDA231ERb_E2_NFkB_rep2


title: MDA231ERb_veh_NFkB_rep2

value: vehicle


title: P21_S6


title: P23_S8


title: MDA231ERb_E2_NFkB_rep1


title: MDA231ERb_veh_NFkB_rep1


title: P11S_S16


title: P14S_S19


title: P22_S7


title: P13S_S18


title: P12S_S17


title: P15S_S20


title: Con3ExoS3_new

value: Helathy Primary PBMCs


title: RJ005C


title: MDA231ERb_veh_RNAPIIpS2

description: E3-MDA_1-pol-21.FCHWYW5BBXX_L2_ITCGAGCGT


title: Con3ExoNoTSOS3


title: Con3Exo_new


title: MDA231ERb_E2+TNFa_H3K27ac_rep2


title: RJ022C


title: MDA231ERb_E2+TNFa_H3K27ac_rep1


title: Con3ExoHeat


title: MDA231ERb_TNFa_H3K27ac_rep2


title: MDA231ERb_TNFa_H3K27ac_rep1


title: MDA231ERb_E2_H3K27ac_rep2


title: Con3ExoHeatS3


title: MDA231ERb_E2_H3K27ac_rep1


title: MDA231ERb_veh_H3K27ac_rep1


title: MDA231ERb_TNFa_H3K27me3_rep2


title: MDA231ERb_veh_H3K27me3_rep1


title: MDA231ERb_E2+TNFa_H3K27me3_rep1


title: MDA231ERb_veh_H3K27me3_rep2


title: 901-PD1pos-B RNASeq

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

description: transcriptomics of B cells.

data_processing:
QC with Fastqc
pseudoalignment with kallisto (command parameters: --single -l 200 -s 30 )
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab delimited text, gene level counts.

source_name: PD1 positive B cells from RA Patients

growth_protocol: B cells were isolated by magnetic bead cell sorting using negative (human B cell isolation kit II, Miltenyi Biotech) or positive selection on the basis of CD19 expression (CD19 microbeads human, Miltenyi) according to the manufacturer’s instructions. Purity of the isolated B cells was routinely checked by flow cytometric analysis for the detection of the B cell marker CD20 and was over 90%. Isolated B cells were then cultured in cRPMI (RPMI (Glutamax-Thermofisher), supplemented with 10% FBS (Sigma), 1000 U/ml Pen/Strep (Sigma)) in a 5% CO2 humidified incubator at 37 oC under atmospheric O2 conditions or a humidified hypoxia chamber (5% CO2, 37 oC) at 3% O2 as indicated.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Samples were sequenced on an Illumina NextSeq500 instrument using 1x75 bp single end reads, following the manufacturer’s protocols. Each library was loaded to obtain ~50 million reads.

tag: disease state

value: Rheumatoid Arthritis (RA)

tag: cell population

value: PD1 positive B cells


title: MDA231ERb_TNFa_H3K27me3_rep1


title: PBMC10XCOMBINED


title: 901-PD1-B RNASeq

description: transcriptomics of B cells.

source_name: PD1 negative B cells from RA Patients

value: PD1 negative B cells


title: S3Comp1217


title: 171129LovA_D17-9763


title: 880-PD1pos-B RNASeq

description: transcriptomics of B cells.


title: 856-PD1pos-B RNASeq

description: transcriptomics of B cells.


title: A1V2_PBMCs


title: 880-PD1-B RNASeq

description: transcriptomics of B cells.


title: MDA231ERb_veh_H3K27ac_rep2


title: Cord Blood CD19+ B cells [CB5]

first: Hector

last: Cordero

address: 650W 168th Street

institute: Columbia University

data_processing:
Illumina software was used for base-calling
Reads were aligned using STAR aligner v2.5.2b to map the reads to the reference human genome (GRCh38)
Normalized counts were generated using DESEeq2 package for differential expression analysis (Love et al., 2014)
sva package was used for batch correction (Leek et al., 2019)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cord Blood

growth_protocol: B cells were obtained from neonatal thymuses and cord blood unidentified samples

extract_protocol:
Total RNA extraction was performed RNAeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using the NEBNext Ultra RNA Library Preparation kit with PolyA selection workflow.

treatment_protocol: B cells were isolated by magnetic cell sorting with EasySep Human B Cell Enrichment Kit (Stem Cell Technologies) following the manufacturer’s instructions and stained in PBS with 2% FCS for 45min with the fluorochrome conjugated antibodies

tag: ID

tag: batch

value: Batch 2

value: Cord Blood CD19+ B cells


title: Cord Blood CD19+ B cells [CB2]

tag: cell type


title: Cord Blood CD19+ B cells [CB1]


title: 846-PD1pos-B RNASeq

description: transcriptomics of B cells.


title: 856-PD1-B RNASeq

description: transcriptomics of B cells.


title: Cord Blood CD19+ B cells [CB4]


title: Cord Blood CD19+ B cells [CB3]


title: MDA231ERb_E2+TNFa_H3K27me3_rep2


title: Thymic CD19+CD21+CD35+ [DP5]

source_name: Thymus

value: Thymic CD19+CD21+CD35+


title: MDA231ERb_E2_H3K27me3_rep2


title: MDA231ERb_E2_H3K27me3_rep1


title: 813-PD1-B RNASeq

description: transcriptomics of B cells.


title: Thymic CD19+CD21+CD35+ [DP4]

value: Batch 1


title: 813-PD1pos-B RNASeq

description: transcriptomics of B cells.


title: Thymic CD19+CD21-CD35- [DN5]

value: Thymic CD19+CD21-CD35-


title: Thymic CD19+CD21-CD35- [DN3]


title: Thymic CD19+CD21+CD35+ [DP3]


title: AHO17-3_D90_CTRL_Hashpool_2

city: Oxford

first: Samuel

middle: Patrick

last: Nayler

address: Sherrington Building, Parks rd

department: Physiology Anatomy and Genetics

institute: Oxford University

description: 2 lanes of sequencing for each of the 4 libraries (2 gex 2 hto)

data_processing:
Paired end fastq.gz files for the human samples each had read 1( R1) of length 26 bp and Read 2 (R2) 98 bp
Sequencing reads were aligned against the GRCh38_premrna build using 10x Cell Ranger v2.2
Digital gene expression matrices (with gene expression counts) for detected cell associated barcodes and unique molecular identifiers (UMIs) were generated by Cell Ranger software (v2.2)
Digital gene expression matrices were analyzed for cell type clustering and identification (Seurat v3.2.1)
Genome_build: GRCh38_premrna
Supplementary_files_format_and_content: barcodes/genes/metadata (.TSV) files and matrix (.MTX) files for each hash pool. Integrated seurat R objects (.RDS)

source_name: iPSC-derived cerebellar organoid

growth_protocol: Subconfluent iPSCs were dissosciated with TrypLE to generate EBs (Embryoid bodies). 1.2E4 cells were washed, spun, counted, resuspended to concentration and deposited into individual wells in ultra-low-attachment 96 well plates (Sumo Bakelite) in growth factor-free chemically defined medium, with Insulin, Rock inhibitor and SB431542. After two days FGF2 was added at 50ng/ml final volume. 1/3 media change was performed without growth factors on day 7 and a full media change was performed at day 14. On day 21 EBs were transferred into Differentiation medium and deposited in low attachment plates with or without encapsulation in Matrigel. Following a further two weeks, organoids were transferred to transwell membranes and allowed to mature at the air liquid interface for 55 days.

extract_protocol: Cell capturing  and library preparation was carried as per kit instructions (Chromium Single Cell Kit [v2 chemistry])

treatment_protocol: One cohort of organoids were embedded in Matrigel on day 21 of culture. Otherwise samples were treated identically.

value: No matrigel embedding on day 21

tag: hashtag

tag: antibodies


title: RJ035C

value: human colorectal cancer tissue


title: Thymic CD19+CD21+CD35+ [DP2]


title: siTAZ2

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: STAR v2.4.0g1
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Customized sample merged reference genome for transcripts assembly with featureCounts: cufflinks cuffmerge
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Genome_build: UCSC human genome model: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: melanoma tumor

growth_protocol: mel537 cells were grown in DMEM with 10% FBS supplementation

extract_protocol:
RNA was collected 2 days post transfection using Direct-zol RNA Miniprep Kit (Zymo Research – R2060).
RNA was harvested using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols RNA-Seq

treatment_protocol: siRNA mediated knockdowns of YAP, TAZ, and YAP/TAZ mel537 melanoma cell were performed using lipofectamine 3000.

value: mel537 melanoma cells

tag: sirna

value: siTAZ


title: AHO17-3_D90_MG_Hashpool_1

value: Matrigel embedding on day 21


title: 846-PD1-B RNASeq

description: transcriptomics of B cells.


title: Thymic CD19+CD21-CD35- [DN2]


title: siYAP2

value: siYAP


title: Thymic CD19+CD21-CD35- [DN4]


title: Thymic CD19+CD21-CD35- [DN1]


title: siYAPTAZ2

value: siYAPTAZ


title: siYAP1


title: siYAPTAZ1


title: siScrambled 1

value: siScrambled


title: TK6_DMSO_Rep1

city: Solna

first: Federico

last: Agostini

state: Stockholm

address: Tomtebodavägen 23a

country: Sweden

institute: Science for Life Laboratories

data_processing:
Library strategy: sBLISS-seq
Reads with the correct structure at the start (8 nt UMI and 8 nt sample barcode) were extracted using scan_for_matches
Reads were mapped to the reference genome (GRCh37/Ensembl v75 for human and GRCm38/Ensembl V90 for mouse) using BWA-MEM. Only reads with mapping quality scores greater than or equal to 60 were retained.
PCR duplicates were filtered out by searching for proximal reads with at most two mismatches in the UMI sequence.
BED files were generated, containing a list of double-strand break (DSB) end genomic locations associated with the number of unique UMIs identified.
To overcome a base mismatch between BAM and BED files, for reads mapping to the - strand the DSB location is shifted -1 nt.
Genome_build: GRCh37/Ensembl v75 for human, GRCm38/Ensembl v90 for mouse
Supplementary_files_format_and_content: BED files containing a list of detected DSB end locations and the associated number of UMIs detected there

source_name: lymphoblastoid cells

extract_protocol:
Cells and nuclei were lysed with mild buffers. After blunting of DSBs and BLISS adapter ligation, DNA was extracted using DNA extraction buffer and proteinase K, followed by phenol/chloroform extraction and ethanol precipitation.
After DNA sonication, genomic DSB ends were amplified with in vitro transcription, after which generated RNA was subjected to an Illumina small RNA-like library preparation protocol (similar to the one described for BLISS in Yan et al, Nature Communications 2017).

value: lymphoblastoid cells


title: siTAZ1


title: TK6_DMSO_Rep2


title: TK6_ETO_Rep2


title: EuLe14

tag: subset

tag: Sex

value: Female


title: Sample 12_RNA-Seq_low_cortisol

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer

data_processing:
After quality control and filtering of raw data, clean reads were aligned to the bovine reference genome (ARS-UCD1.2) using STAR v2.7.3, a splice aware aligner.
featureCounts (Subread package v1.6.5) was used to count the read numbers mapped to each gene.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: For each sample were generated a count file with number of reads overlapping gene regions.

organism: Bos taurus

source_name: Blood cells

growth_protocol: Blood was sampled form the tail vein in one PAXgene Blood RNA System tube (Preanalytix, Hombrechtikon, Switzerland)  for analysis. The PAX gene tubes were handled and stored following the manufacturer’s instructions for RNA extraction. Body condition score (BCS) of each cow was also recorded using a scale from 1(thin) to 5 (fat) with 0.25 point intervals. Cows were ranked on the basis of cortisol in the milk and the 10 cows with the higher and the 10 cows with the lower concentrations were selected for transcriptome analysis.

extract_protocol:
Blood samples collected in the PAX gene Blood RNA Tubes (PreAnalytiX GmbH, Switzerland) were frozen 4 h after the collection and stored at -80 °C until the RNA isolation. Prior to RNA isolation, blood samples were thawed at +4 °C for at least 12 h. RNA was isolated according to PAX gene Blood RNA Kit (PreAnalytiX GmbH, Switzerland) protocol. Quantity and quality of RNA was analysed with Agilent 2100 Bioanalyzer (Agilent Technologies, United States) before sequencing and the RNA integrity number (RIN) score was  ≥ 7 for all the samples. Since the RNA-Seq is highly reproducible within a large dynamic range of detection and provides an accurate estimation of RNA concentration in peripheral whole blood, globin depletion was avoided, as it could significantly reduce the amount and quality of isolated RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Italian Red Pied

tag: tissue

value: blood

value: low cortisol


title: Thymic CD19+CD21+CD35+ [DP1]


title: Sample 13_RNA-Seq_low_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 7_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 10_RNA-Seq_low_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 8_RNA-Seq_low_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: TK6_ETO_Rep1

tag: cell line


title: Sample 9_RNA-Seq_low_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 4_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 6_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: siScrambled 2


title: Sample 5_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 20_RRBS_low_cortisol

data_processing:
Preliminary quality control of raw reads was carried out with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina raw sequences were then filtered with Trimmomatic software v.0.38 to remove adapters and low-quality bases at the sequences end using a sliding window approach.
Bismark software (version 0.22.1) was used to align each bisulfite-treated reads to the bovine reference genome (ARS-UCD1.2) with option -N 1 (maximum number of mismatches allowed)
Sequence reads that produced a unique best alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence, and the methylation state of all cytosine positions in the reads was inferred using the Bismark_methylation_extractor function (cov file). The same reads that aligned to the same regions of the genome were regarded as duplicated reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: For each sample were generated a tab-delimited cov file with methylation call for every single position including the following fileds: chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

growth_protocol: Blood was sampled form the tail vein in a tube with K3-EDTA (Venoject, Terumo Europe N.V., Leuven, Belgium) for analysis.The K3-EDTA tubes were centrifuged within 1 h at 755 x g for 10 min at 20°C and the blood cells stored at –20°C. for DNA analysis. Body condition score (BCS) of each cow was also recorded using a scale from 1(thin) to 5 (fat) with 0.25 point intervals. Cows were ranked on the basis of cortisol in the milk and the 10 cows with the higher and the 10 cows with the lower concentrations were selected for epigenome analysis.

extract_protocol:
DNA was extracted from CD4+ cells following the QIAamp DNA Blood Midi Kit (Qiagen) procedures.
Libraries were prepared using the NEB Next Ultra DNA library preparation kit for Illumina and methylated adapters. Subsequently, size‐selected (150-175 bp and 175-225 bp) and adapter ligated fragments were bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research). Fourteen cycles of PCR were performed and the products were purified using AMPureXP beads.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were used for cluster generation and subsequent sequencing on Illumina HiSeq2500 PE 2x50bp (NXT-Dx Ghent, Belgium, http://www.nxt-dx.com/)

value: Blood cells

tag: milk cortisol


title: Sample 2_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 17_RRBS_low_cortisol


title: Sample 18_RRBS_low_cortisol


title: Sample 19_RRBS_low_cortisol


title: Sample 3_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 11_RRBS_low_cortisol


title: Sample 10_RRBS_high_cortisol

value: high cortisol


title: Sample 14_RRBS_low_cortisol


title: Sample 16_RRBS_low_cortisol


title: Sample 11_RNA-Seq_low_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 7_RRBS_high_cortisol


title: Sample 13_RRBS_low_cortisol


title: Sample 15_RRBS_low_cortisol


title: Sample 8_RRBS_high_cortisol


title: Sample 1_RRBS_high_cortisol


title: Sample 6_RRBS_high_cortisol


title: Sample 2_RRBS_high_cortisol


title: M15_S5

organism:
Homo sapiens
Mus musculus

tag: genome build

value: Cell Line

value: HEK293 and NIH/3T3


title: Sample 1_RNA-Seq_high_cortisol

description: RNA-Seq_Illumina Hi-Seq 2500_Sequencer


title: Sample 5_RRBS_high_cortisol


title: Sample 4_RRBS_high_cortisol


title: Sample 12_RRBS_low_cortisol


title: M14S_S14

tag: sample type


title: Sample 3_RRBS_high_cortisol


title: Sample 9_RRBS_high_cortisol


title: M14_S4

tag: condition


title: M13_S3


title: M12S_S12


title: M11S


title: Con6Exo


title: M12_S2


title: M13S_S13


title: CF1903_Rep_3

first: Francis Amrit Raj

last: Gandhi

address: 4401 Penn Ave

institute: University of Pittsburgh

data_processing: Data was processed using the CLC Genomics Workbench RNA-Seq workflow

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: All strains were maintained by standard techniques on nematode growth medium (NGM) plates seeded with a lawn of E. coli strain OP50. Animals were grown at 25°C until day 1 of adulthood and then transferred to 20°C, a day prior to RNA isolation.

extract_protocol:
Animals were pelleted using M9 buffer, subjected to 7 freeze thaw cycles, and RNA was harvested using Trizol method. RNA was then checked for quality and quantity using the Agilent Tapestation and Qubit Fluorometry.
RNA libraries were prepared for sequencing using the TruSeq stranded mRNA (PolyA+) kit following standard Illumina protocols

tag: genotype

tag: age

value: Day 2 Adult


title: AGP22_Rep_4


title: M11_S1


title: CF1903_Rep_1


title: AGP22_Rep_1


title: Con6ExoNoTSOS3


title: NCH601 shCtrl Repl.1

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

data_processing:
Raw sequencing data was mapped to human genome (assembly version Genome Reference Consortium Human build 38, GRCh38) using Bowtie v2-2.3.2.
Transcript abundance was evaluated with HTSeq v0.6.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files that contain the raw sequence counts for each gene (Ensembl gene identifier).

source_name: Glioblastoma multiforme

extract_protocol:
Total RNA were extracted using the Qiagen’s RNeasy Plus Mini Kit according to supplied protocols. Quality and quantity of samples were measured with Nandrop and Qubit High Sensitivity Kit. RNA integrity was determined using the Agilent Bioanalyzer with the RNA 6000 Nano Kit.
TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols

value: Glioblastoma multiforme

tag: genotype/variation

value: control


title: NCH601 shZFAND3-2 Repl.2


title: NCH601 shCtrl Repl.2


title: NCH601 shZFAND3-1 Repl.1


title: NCH601 shZFAND3-1 Repl.3


title: NCH601 shZFAND3-1 Repl.2


title: NCH601 shZFAND3-2 Repl.1


title: AGP22_Rep_2

city: Pittsburgh


title: M15S_S15


title: CF1903_Rep_2


title: Con6ExoS3


title: K562-HEK293T scATAC-Seq Mix

city: Aachen

first: Mahmoud

middle: M

last: Ibrahim

address: Pauwelsstraße 30

department: Faculty of Medicine

country: Germany

institute: RWTH Aachen University

description: K562 cells and HEK293T cells were mixed in a 7:3 ratio

data_processing:
Raw fastq files were produced and processed using Cell Ranger ATAC version 1.0 (10X Genomics). R1 is mate 1, R2 are cell barcodes and R3 is mate 2.
Fragments were counted across 5kb genomic bins from the "possorted.bam" file from Cellranger using snaptools version 1.4.7 (Fang et al. 2019).
Genome_build: hg38
Supplementary_files_format_and_content: The genomic bin counts before binarization are saved in matrix market format. Cell barcodes and row names (genomic bin coordinates) are provided as two additional text files (colnames.txt and rownames.txt)

source_name: K562 and HEK293T cell lines

growth_protocol: Cells were grown to log growth phase in RPMI media and DMEM+glutamax media respectively supplemented with 10% FBS

extract_protocol:
Nuclei were isolated according to the Corces et al. 2015 (omni-ATAC) protocol and resuspended in 10X Genomics nuclei buffer. The 10X scATAC-Seq user manual for version 1 was followed
Libraries were constructed according to scATAC-Seq user manual version 1. 10 PCR cycles were used in the exponential PCR phase

tag: scatac-seq platform

value: 10X Genomics scATAC version 1


title: NCH601 shCtrl Repl.3

tag: cell type


title: NCH601 shZFAND3-2 Repl.3


title: CF1903_Rep_4


title: 579-rest-B_S4_R1_001.bowtie.bam

city: New York

first: Marc-Werner

last: Dobenecker

address: 1230 York Ave, Box 301

institute: The Rockefeller University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fastq reads were aligned to the mouse reference genome mm9 using Tophat
Subsequently, the cufflinks RNA-seq analysis tool cuffdiff was used to assess differential gene expression, alternative promoter usage, and splicing variation between experimental datasets. The resulting fpkm values were used for further data analysis and visualization.
genome build: mm9

source_name: resting splenic B cells

extract_protocol:
Naïve splenic B cells were freshly isolated (CD43 depleted) and total RNA was harvested RNA with an RNase minikit (Qiagen) according to the manufacturer’s protocol ), and libraries were prepared with the ScripSeq v2 RNA-Seq Library Prepapration kit (Epicentre Biotechnologies) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: resting splenic B cells


title: 577-rest-B_S2_R1_001.bowtie.bam


title: 955-H3K36me2-naive_S5_R1_001.bowtie.bam

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7
Reads were kept if they aligned with two errors or fewer and did not align to more than one location in the genome. A 25-bp density coverage map was created by extending each read for 100 bp to account for mean library fragment length and mapping the number of reads per 25 bp bin using IGVtools
Values in each sample were normalized to fpkm values by calculating the fraction of mapped reads per bin in one million total reads.
genome build: mm9

growth_protocol: feshly isolated (CD43 depleted) naïve splenic B cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to an in house protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: 3 biological replicates of wt or Cre-mediated deletion of the SET-domain of NSD2

tag: chip-ab

value: Millipore, 07-369


title: 578-rest-B_S3_R1_001.bowtie.bam


title: 580-rest-B_S5_R1_001.bowtie.bam


title: AGP22_Rep_3


title: 581-rest-B_S6_R1_001.bowtie.bam


title: TS543_ICRF_H3K9me3

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

source_name: TS543 glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

value: TS543 glioma cells

tag: agent

value: ICRF

tag: chip antibody


title: 954-H3K36me2-naive_S4_R1_001.bowtie.bam


title: 943-H3K36me2-naive_S1_R1_001.bowtie.bam


title: TS543_ICRF_H3K4me3


title: 576-rest-B_S1_R1_001.bowtie.bam


title: TS543_ICRF_H3K27Ac


title: 1012-H3K36me2-naive_S6_R1_001.bowtie.bam


title: Enterocyte_High_M2

source_name: enterocytes isolated from jejunum

value: enterocytes

tag: cell markers

value: Cd73/Nt5e high


title: Enterocyte_Mid_M2

value: Cd73/Nt5e mid


title: TS543_ICRF_H3K4me2


title: Enterocyte_High_M1


title: TS543_DMSO_H3K4me1

value: DMSO


title: TS543_ICRF_H3K36me3


title: TS543_DMSO_H3K4me3


title: TS543_DMSO_H3K9me3


title: TS543_ICRF_H3K27me3


title: TS543_DMSO_H3K4me2


title: TS543_DMSO_H3K27Ac


title: TS543_DMSO_H3K36me3


title: 1010-H3K36me2-naive_S3_R1_001.bowtie.bam


title: Enterocyte_Mid_M1


title: 953-H3K36me2-naive_S2_R1_001.bowtie.bam


title: MUT Lm-T4 RNA-Seq rep2

city: Bronx

first: Shu Shien

last: Chin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: unstimulated memory CD8 T cells

data_processing:
RNAseq reads were aligned to the Mouse reference mm10 with STAR (v2.4.2a)
Gene quantification was performed using featureCounts (v1.4.3) / Transcripts were quantified using Kalisto
Normalization and Comparative analysis were performed with DESeq2 (v 1.10.1)

source_name: Spleen

extract_protocol:
1,000 memory OT-I cells were flow-sorted into lysis buffer (Takara Bio USA) based on congenic markers after enrichment for CD8+ T cells (negative selection).  cDNA was synthesized and amplified directly from intact cells using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA) according to the manufacturer protocol.
Illumina cDNA library was prepared using Nextera XT DNA Library Preparation Kits according to manufacturer protocol.

value: OT-I CD8 T cell

value: Il2ra mut/mut


title: MUT Lm-T4 RNA-Seq rep4

description: unstimulated memory CD8 T cells


title: WT Lm-T4 RNA-Seq rep3

description: unstimulated memory CD8 T cells

value: Il2ra WT


title: TS543_ICRF_H3K4me1


title: MUT Lm-N4 RNA-Seq rep4

description: unstimulated memory CD8 T cells


title: WT Lm-T4 RNA-Seq rep2

description: unstimulated memory CD8 T cells


title: MUT Lm-T4 RNA-Seq rep1

description: unstimulated memory CD8 T cells


title: WT Lm-T4 RNA-Seq rep4

description: unstimulated memory CD8 T cells


title: MUT Lm-N4 RNA-Seq rep2

description: unstimulated memory CD8 T cells


title: MUT Lm-T4 RNA-Seq rep3

description: unstimulated memory CD8 T cells


title: WT Lm-N4 RNA-Seq rep3

description: unstimulated memory CD8 T cells


title: WT Lm-N4 RNA-Seq rep4

description: unstimulated memory CD8 T cells


title: gcn20 versus Col7 replicate 2

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

hyb_protocol: Hybridization and slide washing were performed with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively.

scan_protocol: slides were scanned in a GenePix 4000B microarray scanner, at 5 μm resolution and using the double scanning

data_processing: Feature Extraction software 9.5.1. was used for background substraction and normalization

organism: Arabidopsis thaliana

label_protocol: Sample RNA (0.5 μg) was amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: Arabidopsis plants were grown on MS plates for 20 days after sowing

extract_protocol: Total RNA extracted using Qiagen RNA extraction kit following manufacturer's instructions

value: wildtype Col7

value: two-weeks old seedlings

value: gcn20 mutant


title: WT Lm-T4 RNA-Seq rep1

description: unstimulated memory CD8 T cells


title: gcn20 versus Col7 replicate 1


title: TS543_DMSO_H3K27me3


title: Enterocyte_Neg_M2

value: Cd73/Nt5e negative


title: gcn20 versus Col7 replicate 3


title: WT Lm-N4 RNA-Seq rep1

description: unstimulated memory CD8 T cells


title: MUT Lm-N4 RNA-Seq rep3

description: unstimulated memory CD8 T cells


title: MUT Lm-N4 ATAC-Seq rep1

description: unstimulated memory CD8 T cells

data_processing:
paired-end reads were trimmed for adaptors and removal of low-quality reads using Trim_galore (v0.3.7)
Reads were mapped to mm10 assmbly using Picard (v1.92)
Reads were filtered to exclude mitochondrial DNA or duplicates using samtools (v0.1.19)
Peak calling using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Peak calling using MACS2

extract_protocol:
Briefly, nuclei were isolated from 15,000-50,000 FACS sorted memory OT-I  cells from host mice using a solution of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630.
Immediately following nuclei isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 45 min at 37C. Transposed DNA fragments were purified using Qiagen MinElute Kit and PCR amplified using NEB Next High Fidelity 2x PCR master mix (New England Labs) with dual indexes primers (Illumina Nextera). The size distribution and molarity of the sequencing library were determined by using an Bioanalyzer analysis (High Sensitivity DNA chip, Agilent).


title: WT Lm-N4 ATAC-Seq rep1

description: unstimulated memory CD8 T cells


title: WT Lm-N4 ATAC-Seq rep2

description: unstimulated memory CD8 T cells


title: MUT Lm-T4 ATAC-Seq rep1

description: unstimulated memory CD8 T cells


title: WT Lm-T4 ATAC-Seq rep2

description: unstimulated memory CD8 T cells


title: Sample 9-Pt1

city: Saint Louis

first: Govindaswamy

last: Chinnadurai

state: MO

address: 1100 S. Grand Blvd.

department: Molecular Microbiology and Immunology

institute: Saint Louis University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Neuron

growth_protocol: iPSCs were derived using Cytotune Sendai virus (Sev) reprogramming vectors according to the protocol provided by  ThermoFisher. To generate Neural Stem Cells (NSCs), the iPSCs were plated on Geltrex coated plates and grown with Neural induction media for 7 days. The neural induction media was composed of Neurobasal Medium and Neural Induction Supplement. After 7 days, the NSCs were then grown with Neural Expansion Media for another 5 days. The Neural Expansion Media was composed of Neurobasal Medium, Advanced DMEM/F-12, and neural induction supplement.  In order to differentiate the NSCs to neurons, they were first plated on Poly-ornithine and laminin-coated plates, and grown using NSC Serum Free Media (SFM) (ThermoFisher Scientific). For the first two days, they were grown in NSC SFM with Poly-ornithine and laminin coated plates. The NSC SFM was composed of Knockout DMEM/F-12, Stempro  Neural Supplement, Recombinant FGF-Basic (Human), GlutaMAX™-I Supplement, and recombinant EGF (Human). After two days, they were grown in differentiation medium, which was composed of 1X neurobasal medium, serum free B-27 supplement, and GlutaMAX™-I supplement.

extract_protocol:
Total RNA was isolated from iPSC-derived neurons (14 days differentiation). Cells were lysed with Trizol (Zymo Research, Irvine, CA), and total RNA was purified using the Direct-Zol RNA kit (Zymo Research, Irvine, CA) following the manufacturer's protocol. RNA concentration was determined by NanoDrop spectrophotometer.
Library preparation was performed with 1 ug of total RNA, integrity was determined using an Agilent tapestation. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina). mRNA was then fragmented in buffer containing 40 mM Tris Acetate pH 8.2, 100 mM Potassium Acetate and 30 mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

value: Neuron differentiated from iPSC


title: MUT Lm-N4 RNA-Seq rep1

description: unstimulated memory CD8 T cells


title: Sample 11-Pt2


title: Sample 10-Pt2


title: Enterocyte_Neg_M1


title: MUT Lm-N4 ATAC-Seq rep2

description: unstimulated memory CD8 T cells


title: Sample 4-Ct2

growth_protocol: iPSCs were derived using Cytotune Sendai virus (Sev) reprogramming vectors according to the protocol provided by  ThermoFisher. To generate Neural Stem Cells (NSCs), the iPSCs were plated on Geltrex coated plates and grown with Neural induction media for 7 days. The neural induction media was composed of Neurobasal Medium and Neural Induction Supplement. After 7 days, the NSCs were then grown with Neural Expansion Media for another 5 days. The Neural Expansion Media was composed of Neurobasal Medium, Advanced DMEM/F-12, and neural induction supplement.  In order to differentiate the NSCs to  neurons, they were first plated on Poly-ornithine and laminin-coated plates, and grown using NSC Serum Free Media (SFM) (ThermoFisher Scientific). For the first two days, they were grown in NSC SFM with Poly-ornithine and laminin coated plates. The NSC SFM was composed of Knockout DMEM/F-12, Stempro  Neural Supplement, Recombinant FGF-Basic (Human), GlutaMAX™-I Supplement, and recombinant EGF (Human). After two days, they were grown in differentiation medium, which was composed of 1X neurobasal medium, serum free B-27 supplement, and GlutaMAX™-I supplement.


title: Sample 6-Ct3


title: MUT Lm-T4 ATAC-Seq rep2

description: unstimulated memory CD8 T cells


title: Sample 3-Ct1


title: Sample 7-Pt1


title: Sample 5-Ct2


title: Sample 12-Pt2


title: ChIPseq_F1_Input_rep2

city: Bunkyo-ku

first: Taiko

middle: Kim

last: To

state: Tokyo

address: 7-3-1 Hongo

department: Biological Science

institute: University of Tokyo

data_processing:
WGBS: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). Mapping to the reference genome (TAIR10), deduplication, and methylation extraction were performed using Bismark version 0.10.1 (Krueger and Andrews, 2011). The parameters used for mapping is -n 1 –l 20 –e 90. Uniquely aligned reads were used and reads with more than one alignment with same read quality were removed.
RNA-seq: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). The quality filtered reads were mapped to genes (TAIR10) were counted through STAR algorithm (Dobin et al., 2013).
ChIP-seq: The reads were quality-filtered using Trimmomatic (Bolger et al. 2014) and mapped to TAIR10 genome using Bowtie (Langmead et al., 2009) with option -M 1 --best.
Genome_build: TAIR10
Supplementary_files_format_and_content: WGBS: CX_report file
Supplementary_files_format_and_content: RNA-seq: STAR ReadsPerGene output file
Supplementary_files_format_and_content: ChIP-seq: bowtie output file

source_name: seedling

growth_protocol: RNA-seq and ChIP-seq: Seedlings were grown on MS medium with 1% sucrose and 0.8% agar with 16h light / 8h dark.

extract_protocol:
ChIP-seq: Sixteen-days of seedlings grown on MS Agar plates were frozen in liquid nitrogen, ground, and fixed in 0.5% formaldehyde. Nuclei isolation, micrococcal nuclease (SIGMA N3755) treatment, nuclear membrane disruption were followed by centrifugation to extract the supernatant for immunoprecipitation. After affinity purification, DNA was reverse-crosslinked and purified.
ChIP-seq: Libraries were prepared using SMARTer ThruPLEX DNA-seq Kit according to the manufacturer’s instruction.

value: seedling


title: Sample 2-Ct1


title: WT Lm-N4 RNA-Seq rep2

description: unstimulated memory CD8 T cells


title: WT Lm-T4 ATAC-Seq rep1

description: unstimulated memory CD8 T cells


title: ChIPseq_F1_H2AW7_rep2


title: Sample 8-Pt1


title: ChIPseq_F1_Input_rep1


title: MCF7_ARID1B_E2_Chipseq

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

source_name: breast cancer cells

growth_protocol: MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors using  KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.

treatment_protocol: Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatemnt of either 100 nM 17β-estrodial (E2) or ethanol as vehcile control for 1hr.

tag: treatment

value: E2 (one hour)

value: ARID1B(Bethyl, A301-046A)


title: A549P4_control_S7

first: Chun-Lin

last: Lin

state: Texas

address: 7703 Floyd Curl Dr., MC8257, 233 STRF

institute: University of Texas Health Science Center at San Antonio

data_processing:
Illumina Real-Time Analysis software used for basecalling.
Sequenced reads were mapped to GRCh38 human genome using STAR-2.5.3a
Fragments Per Kilobase of transcript per Million mapped reads were calculated for each sample using RSEM software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample ...

source_name: A549 lung cancer cell line

growth_protocol: A549 lung cancer cell line cells were cultured in F12K medium with 10%FBS and 1% penicillin/streptomycin aired with 5%CO2 at 37oC

extract_protocol:
Total RNA was extracted from TP-0903–treated and AXL-knockdown A549 cells and from respective controls in biological replicates by using the PureLink RNA Mini Kit
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.

treatment_protocol: 40 nM TP-0903 and AXL-knockdown


title: MCF7_E2_ATACseq

data_processing:
Basecalls performed using Illuminal CASAVA software.
The adaptor was removed by using cutadapt v1.11 with parameters "-m 20 -e 0.1". The clean reads were aligned to the hg19 genome assembly using bowtie2 v2.2.9 with parameters "-mm --very-sensitive --no-discordant -X 2000", and only primary alignments were retained. The alignments were shifted with +4 for plus strand and -5 for minus strand.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

extract_protocol: 20,000 cells were harvested for each condition. After purification of nuclei, transposition was performed with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030). ATAC-seq library prep was performed as in Buenrostro et al, 2015.


title: A549P3_control_shRNA_S3


title: A549P15_AXL_shRNA_S2


title: ChIPseq_suvh456_Input_rep2

value: suvh4 suvh5 suvh6

tag: tissue


title: ChIPseq_suvh456_H2AW7_rep1


title: ChIPseq_F1_H2AW7_rep1


title: A549P4_TP0903_S8

tag: cell line


title: ChIPseq_F1_H2AZ_rep2


title: MCF7_ARID1B_Veh_Chipseq

value: Vehicle (one hour)


title: Sample 1-Ct1


title: ChIPseq_F1_H2AW6_rep2


title: ChIPseq_F1_H2AZ_rep1


title: ChIPseq_F1_H2AW6_rep1


title: ChIPseq_suvh456_H2AZ_rep2


title: A549P3_AXL_shRNA_S4


title: HT29_DTB_12hrD_87_S118

source_name: HT29 colorectal cancer cell line

growth_protocol: HT29 colorectal cancer cell line cells  were cultured in RPKM-1604 medium with 10%FBS and 1%  1% penicillin/streptomycin aired with 5%CO2 at 37oC

extract_protocol:
single cell cDNA generation with Fluidigm C1 Single-Cell Auto Prep System
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.
single cell RNA-seq

treatment_protocol: Double thymidine block and 100 nM dasatinib

value: dasatinib


title: A549P15_control_shRNA_S1


title: ChIPseq_suvh456_Input_rep1


title: A549P17_control_S5


title: ChIPseq_suvh456_H2AZ_rep1


title: ChIPseq_suvh456_H2AW7_rep2


title: HT29_DTB_12hrD_52_S124


title: ChIPseq_suvh456_H2AW6_rep2


title: A549P17_TP0903_S6


title: ChIPseq_suvh456_H2AW6_rep1


title: MCF7_Veh_ATACseq


title: ChIPseq_cmt23_H2AW7_rep1

value: cmt2 cmt3


title: HT29_DTB_12hrD_45_S120


title: HT29_DTB_12hrD_48_S112


title: HT29_DTB_12hrD_43_S134


title: ChIPseq_cmt23_Input_rep1


title: HT29_DTB_12hrD_47_S128


title: ChIPseq_cmt23_Input_rep2


title: HT29_DTB_12hrD_41_S127


title: ChIPseq_cmt23_H2AZ_rep1


title: HT29_DTB_12hrD_40_S103


title: ChIPseq_WT_Input_rep1

value: Wild-type


title: HT29_DTB_12hrD_44_S96


title: HT29_DTB_12hrD_39_S119


title: HT29_DTB_12hrD_46_S104


title: HT29_DTB_12hrD_37_S133


title: HT29_DTB_12hrD_38_S95


title: ChIPseq_cmt23_H2AW7_rep2


title: ChIPseq_cmt23_H2AW6_rep1


title: ChIPseq_cmt23_H2AW6_rep2


title: HT29_DTB_12hrD_35_S126


title: ChIPseq_WT_H2AW7_rep2


title: ChIPseq_WT_H2AW7_rep1


title: HT29_DTB_12hrD_32_S94


title: ChIPseq_WT_H2AW6_rep1


title: ChIPseq_cmt23_H2AZ_rep2


title: ChIPseq_WT_H2AZ_rep1


title: ChIPseq_WT_Input_rep2


title: HT29_DTB_12hrD_31_S132


title: ChIPseq_WT_H2AZ_rep2


title: HT29_DTB_12hrD_36_S110


title: HT29_DTB_12hrD_29_S125


title: RNAseq_h2az_CMT23_rep1

extract_protocol:
RNA-seq: Total RNAs were purified from 12-day-old plants grown on MS Agar plates using RNeasy Plant Mini Kit (QIAGEN), and then treated with DNase I (TaKaRa)
RNA-seq: RNA Fragmentation was performed at 94°C for 7 min. Libraries were constructed using the KAPA Stranded RNA-seq Library Preparation Kit according to the manufacturer’s instruction.

value: hta8 hta9 hta11


title: ChIPseq_WT_H2AW6_rep2


title: HT29_DTB_12hrD_30_S109


title: HT29_DTB_12hrD_28_S101


title: HT29_DTB_12hrD_27_S117


title: HT29_DTB_12hrD_34_S102


title: RNAseq_h2az_cmt23_rep2

value: cmt2 cmt3 hta8 hta9 hta11


title: RNAseq_cmt23_h2az_rep1


title: HT29_DTB_12hrD_24_S100


title: RNAseq_cmt23_H2AZ_rep2


title: RNAseq_F1_rep1


title: RNAseq_h2az_cmt23_rep1


title: HT29_DTB_12hrD_20_S92


title: HT29_DTB_12hrD_17_S123


title: HT29_DTB_12hrD_18_S99


title: HT29_DTB_12hrD_19_S116


title: HT29_DTB_12hrD_21_S131


title: HT29_DTB_12hrD_22_S108


title: HT29_DTB_12hrD_26_S93


title: RNAseq_cmt23_h2az_rep2


title: HT29_DTB_12hrD_16_S107


title: RNAseq_suvh456_rep1


title: RNAseq_h2az_CMT23_rep2


title: RNAseq_cmt23_rep1


title: HT29_DTB_12hrD_14_S91


title: HT29_DTB_12hrD_42_S111


title: RNAseq_Col_rep1


title: RNAseq_suvh456_rep2


title: RNAseq_cmt23_rep2


title: RNAseq_F1_rep2


title: HT29_DTB_12hrD_12_S98


title: MHY1-overexpressing

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI Reference genome (Y. lipolytica CLIB122)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Yarrowia lipolytica

growth_protocol: Y. lipolytica cells were grown in 50 ml YNDC7 liquid medium supplemented with uracil to a final OD600 of 0.8 at 30℃.

extract_protocol:
Total RNA was extracted using Yeast RNA Kit (Omega, China)
RNA libraries were prepared for sequencing using standard Illumina protocols.A total amount of 1 µg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using TruSeq RNA Library Preparation Kit (Illumina, USA) following manufacturer’s recommendations.

value: MHY1-overexpressing mutant strain


title: HT29_DTB_12hrD_11_S122


title: HT29_DTB_12hrD_10_S106


title: RNAseq_Col_rep2


title: HT29_DTB_12hrD_08_S90


title: HT29_DTB_12hrD_15_S130


title: HT29_DTB_12hrD_13_S115


title: HT29_DTB_12hrD_07_S114


title: HT29_DTB_12hrD_06_S97


title: HT29_DTB_12hrD_04_S105


title: HT29_DTB_12hrD_05_S121


title: HT29_DTB_12hrD_01_S113


title: HT29_DTB_12hrD_03_S129


title: HT29_DTB_12hr_46_S158

value: control


title: WT

value: wild-type strain


title: HT29_DTB_12hr_42_S168


title: mhy1

description: mhy1Δ mutant strain

value: mhy1<delta> mutant strain


title: HT29_DTB_12hr_44_S146


title: HT29_DTB_12hr_41_S163


title: HT29_DTB_12hrD_02_S89


title: HT29_DTB_12hr_49_S151


title: HT29_DTB_12hr_39_S149


title: HT29_DTB_12hr_40_S157


title: HT29_DTB_12hr_37_S142


title: HT29_DTB_12hr_52_S136


title: HT29_DTB_12hr_31_S141


title: HT29_DTB_12hr_48_S135


title: HT29_DTB_12hr_28_S155


title: HT29_DTB_12hr_26_S144


title: HT29_DTB_12hr_25_S140


title: SN14-2

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000004515.4_Glycine_max_v2.0
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Glycine max

source_name: SOYBEAN

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: L-1-OL-1 were planted in the experimental field under natural conditions at the industrial crops institute, Heilongjiang Academy of Agricultural Sciences (Harbin, China).

value: LEAF


title: SN14-3


title: HT29_DTB_12hr_38_S145


title: HT29_DTB_12hr_22_S166


title: SN14-1


title: HN44-3


title: lung tissue H4

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by SeqPrep and Sickle, then mapped to hg19 whole genome using Hisat2
Transcriptome was assembled using Stringtie, then Reads Per Kilobase of exon model per Million mapped reads(RPKM) were calculated using Ballgown.
Significantly differentially expressed mRNAs were selected using DEGseq with following condition: qvalue<0.05 && |log2FC|>1
IncRNA was filtered by CPC (Coding Potential Calculator) < 0 , CNCI (Coding-Non-Coding Index) < 0 , CPAT (Coding Potential Accessment Tool) with low coding potential and not significat in Pfam.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol: Total RNA of each lung sample was extracted by using TRIzol Reagent (Invitrogen, US) and further purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, USA), NanoDrop (Thermo Fisher Scientific Inc., USA) and 1% agarose gel. Total RNA (1 μg) with the value of RNA integrity number (RIN) > 7 was used for library preparation of the following next generation sequencing, with the NEBNext Ultra II Directional RNA Library Prep. Kit for Illumina. The rRNA was depleted from total RNA using Ribo-Zero™ rRNA removal Kit (Illumina, USA), and cDNA libraries were generated following manufacture’s protocols. Then, libraries with different indices were multiplexed and loaded on Illumina HiSeq instrument (Illumina, USA) for 2 × 150 paired-end sequencing according to manufacturer’s instructions.

treatment_protocol: All the subjects were confirmed as pulmonary tuberculosis by pathological examination with sputum smear and culture negative preoperatively, and accompanied by tuberculous pleurisy or other extrapulmonary tuberculosis.

tag: metabolic activity

value: high metabolic activity

tag: gender

value: Female

tag: clinical diagnosis

value: Secondary pulmonary tuberculosis with multi-drug resistance


title: lung tissue L4

value: low metabolic activity


title: lung tissue H3

value: Multi-drug resistant tuberculosis, and left side chest wall tuberculosis with sinus formation


title: lung tissue L2

value: Pulmonary tuberculosis, and spinal tuberculosis


title: HT29_DTB_12hr_36_S167


title: HT29_DTB_12hr_18_S153


title: HN44-2


title: HT29_DTB_12hr_34_S156


title: HT29_DTB_12hr_45_S150


title: lung tissue L5

value: Pulmonary tuberculosis, and tuberculous pleurisy


title: HT29_DTB_12hr_23_S162


title: Rat LEC at 2W

city: Kahoku

first: Eri

last: Kubo

state: Ishikawa

address: 1-1 Daigaku, Uchinada

department: Ophthalmology

institute: Kanazawa Medical University

description: Gene expression data from Rat LECs at 2W after ECLE

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in theGene Chip® Fluidics Station 450.

scan_protocol: Air-dried slides were scanned with a GeneChip® Scanner 3000 7G.

data_processing: Scanned images were analyzed with AGCC（Affymetrix® GeneChip® Command Console®) Software and Affymetrix® Expression Console™.

label: biotin

organism: Rattus norvegicus

source_name: Rat LECs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lens epithelial cells from 7, 8 and 9 weeks-old Rat after ECLE

extract_protocol: Animals were sacrificed at either 0 (after the surgery was completed) (Day 0), 7 (1W), or 14 days (2W) after surgery, via a lethal dose of CO2. Lens capsules with LECs were removed from all eyes as PCO samples.

treatment_protocol: ECLE was performed in 7 weeks-old rats. At Day0, 1W and 2W after ECLE, LECs was collected.

value: 2W after ECLE

value: LECs


title: HT29_DTB_12hr_14_S143


title: lung tissue H5


title: Rat LEC at Day0

description: Gene expression data from Rat LECs at Day0 after ECLE

value: Day0 after ECLE


title: HT29_DTB_12hr_15_S139


title: lung tissue H2


title: Rat LEC at 1W, biological rep1

description: Gene expression data from Rat LECs at 1W after ECLE

value: 1W after ECLE


title: Rat LEC at 1W, biological rep2


title: HT29_DTB_12hr_13_S148


title: lung tissue L1

value: Male

value: Pulmonary tuberculosis


title: HT29_DTB_12hr_11_S160

value: control


title: HT29_DTB_12hr_09_S138


title: lung tissue L3


title: HT29_DTB_12hr_07_S147


title: HN44-1


title: HT29_DTB_12hr_24_S154


title: cKO rep1

first: Lichao

last: Xu

address: luojiashan

data_processing:
Cutadapt (version 1.16, http:// cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were aligned to the mouse reference genome (mm10) using BWA (version 0.7.15, http://bio-bwa.sourceforge.net) with the default settings
Peaks calling was finished by MACS2 (version 2.1.1, https://github.com/taoliu/MACS) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cut- off 1E-10 --extsize 147
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: cortex

extract_protocol:
For each experiment, single-cell suspensions from E13.5 dorsal cortices were collected as described above. Cells were cross-linked for 10 min at room temperature with 1% formaldehyde and then quenched with 0.125 M of glycine for 5 min. Cross-linked samples were then rinsed in PBS twice, and harvested in ice-cold IP buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.1, 5 mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 1× Roche protease inhibitor cocktail, and 1 mM PMSF), followed by sonication in a Bioruptor Pico (Diagenode) at a setting of ‘30s on/ 30s off, 30 cycles’ at 4°C. 20 μl aliquot were taken for checking the efficiency of sonication. After de-crosslinked in de-crosslink buffer (1% SDS, 250mM NaCl in TE buffer) for 3 h, the sample was purified with DNA purification kit (QIAGEN), followed by DNA electrophoresis with 2% agarose gel. 30 μl lysate (3%) was kept to quantify DNA before immunoprecipitation (input). Immunoprecipitation was further performed with sheared chromatin and 3 μg anti-H3K36me3 antibody (abcam, ab9050) overnight at 4°C on a rotating wheel. Next day, immunocomplexes were incubated with 50 μl Protein G sepharose beads for 4 h at 4°C, followed by washing 3 times with wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) and once with wash buffer II (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS). Protein-DNA complexes were de-crosslinked in 120 μl de-crossed buffer (TE buffer) and shaked at 65℃ for 3 h. DNA extraction, precipitation, and resuspension were performed using DNA purification kit (QIAGEN).
ChIP-seq libraries were constructed by StepWise DNA Lib Prep Kit for Illumina (Abclonal RK20202). For each sample, 40 μl purified ChIP DNA (about 300 pg) was end-repaired for dA tailing, followed by adaptor ligation with Full DNA Adapter Kit for Illumina Set_A (Abclonal RK20282). Each adaptor was marked with an index of 6 bp, which can be recognized after mixing different samples together. Adaptor-ligated ChIP DNA was purified by AMPure XP beads (1:1) and then used as template for 16 cycles of PCR amplification. Amplified ChIP DNA was purified again using AMPure XP beads (1:1) in 22 μl low-EDTA TE buffer. For multiplex sequencing, libraries with different index were mixed together with equal molar quantities by considering appropriate sequencing depth (20 million reads per library). Libraries were sequenced by Illumina Hi-seq X Ten platform with pair-end reads of 150 bp.

value: cortex

value: Embryo 13.5

value: Emx1-Cre;Setd2 f f (cKO)

value: anti-H3K36me3 (abcam, cat#ab9050)


title: HT29_DTB_12hr_17_S161


title: lung tissue H1

value: high metabolic activity


title: HT29_DTB_12hr_16_S165


title: Z3 - DZ-66 + P74-3

city: Ottawa

first: Myron

last: Smith

state: Ontario

address: 1125 Colonel By drive

department: Biology

country: Canada

institute: Carleton University

description: NS.1339.004.NEBNext_dual_i7_E12---NEBNext_dual_i5_E12.Z3

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence to about 100bp length. Then mapped to C.parasitica whole genome v.2 using STAR v2.7
Novel transcripts from regions of the genome that showed significant expression, but were not previously annotated as genes were identified using StringTie v.2.1.3
Raw Count table was created using SummarizedExperiment R package.
Genome_build: C.parasitica v.2, FASTA for novel transcripts is available on the series record.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cryphonectria parasitica

source_name: mycelium

extract_protocol:
Cultures for RNA extraction were grown in 8.5 cm Petri plates on potato dextrose agar (PDA, BD Difco Brand, NJ, USA) overlaid with sterile semi-permeable cellophane membranes. Total RNA was extracted using the Qiagen RNeasy Plant RNA extraction kit following manufacturer manual (Qiagen, Valencia, CA, USA) with DNAse treatment step.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mix of DZ-66 + P74-3

value: mycelium


title: X2 - EP155 + P74-3

description: NS.1339.004.NEBNext_dual_i7_164---NEBNext_dual_i5_164.X2

value: mix of EP155 + P74-3


title: Z1 - DZ-66 + P74-3

description: NS.1339.004.NEBNext_dual_i7_D12---NEBNext_dual_i5_D12.Z1


title: Z4 - DZ-66 + P74-3

description: NS.1339.004.NEBNext_dual_i7_F12---NEBNext_dual_i5_F12.Z4


title: X4 - EP155 + P74-3

description: NS.1339.004.NEBNext_dual_i7_165---NEBNext_dual_i5_165.X4


title: P2 - P74-3

description: NS.1326.001.NEBNext_dual_i7_158---NEBNext_dual_i5_158.P2


title: HT29_DTB_12hr_12_S152


title: HT29_DTB_12hr_03_S137


title: Single cell thymic CD19+CD21-CD35- [HE001]

first: Hector

last: Cordero

address: 650W 168th Street

institute: Columbia University

description:
HE001
Single-cell RNA-seq

data_processing:
The sequencing was done using Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions via NovaSeq 6000.
The raw data from each sample were demultiplexed, aligned to the GRCh38-1.2.0. human reference genome.
UMI counts were quantified using the 10X Genomics Cell Ranger pipeline (v2.1.1, 10X Genomics).
Data analysis with the filtered barcode matrix files was done by using the Seurat package version 3.0 (Butler et al., 2018).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *mtx: Matrix table with raw gene counts for every gene and every cell.
Supplementary_files_format_and_content: barcodes*.tsv: Barcode list
Supplementary_files_format_and_content: genes*.tsv: Gene names
Supplementary_files_format_and_content: metrics_summary*.csv: Summary file
Supplementary_files_format_and_content: *.cloupe: Cell Loupe file

source_name: Thymus

growth_protocol: B cells were obtained from neonatal thymuses.

extract_protocol:
Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions.
The libraries were quantified using KAPA hgDNA Quantification and QC Kit (Kapa Biosystems).

treatment_protocol: B cells were isolated by magnetic cell sorting with EasySep Human B Cell Enrichment Kit (Stem Cell Technologies) following the manufacturer’s instructions and stained in PBS with 2% FCS for 45min with the fluorochrome conjugated antibodies.

value: Thymic CD19+CD21-CD35- B cells

value: 4 months


title: Single cell thymic CD19+CD21-CD35- [HE002]

description:
HE002
Single-cell RNA-seq

value: 4 days


title: HT29_DTB_12hr_05_S159


title: P1 - P74-3

description: NS.1326.001.NEBNext_dual_i7_157---NEBNext_dual_i5_157.P1


title: E4 - EP155

description: NS.1326.001.NEBNext_dual_i7_156---NEBNext_dual_i5_156.E4


title: cKO rep2


title: control rep2


title: control rep1


title: D3 - DZ-66

description: NS.1339.004.NEBNext_dual_i7_162---NEBNext_dual_i5_162.D3


title: D2 - DZ-66

description: NS.1339.004.NEBNext_dual_i7_161---NEBNext_dual_i5_161.D2


title: BS_rdr126 suvh456

source_name: Rosette leaves

growth_protocol: WGBS: Plants were grown on soil.

extract_protocol:
WGBS: Genomic DNA was isolated from rosette leaves using the Nucleon Phytopure genomic DNA extraction kit (GE Healthcare).
WGBS: Genomic DNA was fragmented using Covaris S220, and the size between 300-450bp were gel-purified. The libraries were prepared using TruSeq DNA LT Sample Prep Kit (Illumina) and subjected to bisulfite conversion using MethylCode Bisulfite Conversion Kit (Life Technologies). Bisulfite-treated DNA were amplified with KAPA HiFi HotStart Uracil ReadyMix (Kapa Biosystems), and then purified with Agencourt AMPure XP (Beckman Coulter).

value: rdr1 rdr2 rdr6 suvh4 suvh5 suvh6

value: Leaves


title: D1 - DZ-66

description: NS.1339.004.NEBNext_dual_i7_160---NEBNext_dual_i5_160.D1


title: BS_rdr126 cmt23

value: rdr1 rdr2 rdr6 cmt2 cmt3


title: BS_h2az cmt23

value: cmt2 cmt3 hta8 hta9 hta11


title: E3 - EP155

description: NS.1326.001.NEBNext_dual_i7_155---NEBNext_dual_i5_155.E3


title: BS_F1_in_IBM1(ibm1+/- cmt23 X ibm1+/- suvh456)


title: BS_h2az CMT23

value: hta8 hta9 hta11