title: Peripheral blood RNA [A584_095]

extract_protocol: RNA from whole blood was isolated according to the PAXgene Blood RNA Kit manufacturer (BD, Franklin Lakes, NJ, USA), including the optional on-column DNase digestion according to manufacturer’s instructions.


title: Dox  rep3

status: Public on Mar 21 2022

type: SRA

city: Shijiazhuang

first: Yanmin

last: Zou

state: Hebei

address: 286 Huaizhong Road

department: Center for Agricultural Resources Research

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: 7-day-old seedlings

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
Assembly: Arabidopsis thaliana
Supplementary files format and content: tab-delimited text files include reads and FPKM values for each Sample ...

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface-sterilized with 50% (v/v) bleach for 5 min and washed at least four times with sterile water. Sterile seeds were germinated and grown on 1/2 Murashige and Skoog (MS)

extract_protocol:
Total RNA for transcriptome sequencing was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: 7-d-old plants grown in1/2 Murashige and Skoog (MS) medium and then treated with H2O, Dox or EtBr were collected.

tag: tissue

value: Total seedling

tag: genotype

value: wild type (Col-0)

tag: treatment

value: seedling treated with Dox


title: 183B7-25h4

city: Blacksburg

first: Guillaume

last: Pilot

state: VA

address: 220 Ag Quad Lane

department: School of Plant and Environmental Sciences

country: USA

institute: Virginia Tech

description:
BiolRep3
DEX25_cuffdiff_genes.fpkm_tracking

data_processing:
Tophat2 was used for read mapping
Cufflinks for transcript assembly
Cuffdiff2 was used for abundance estimation and identification of significant change in mRNA contents
Comparisons: DEX 7 h vs. 4c-S7 7 h; DEX 25 h vs. 4c-S7 25 h; gdu1-1D vs. Col
Comparisons: GDU2 vs. Col-7, GDU4 vs. Col-7, GDU5 vs. Col-7,  GDU6 vs. Col
Assembly: TAIR 10
Supplementary files format and content: cuffdiff output: genes.fpkm_tracking

source_name: Inducible line treated by DEX. Analyzed 25 h post-treatment

growth_protocol: Plants were grown for 23 days on soil, in a growth chamber (16h/8h light dark), 22C, 120 uE

extract_protocol:
RNA were extracted using the Qiagen Plant RNeasy kit from all leaves from 4 to 6 plants.
Performed by the GeneWiz company in 2013

treatment_protocol: 100 µM dexamethasone + 300 ppm silwet L-77  at 11 am - 5 h after dawn - keeping a humidity dome for 7 h, for inducible (183B7) and control (4c-S7) lines. Not treatment for the constitutuve over-expressors and wild type

value: Leaves

tag: ecotype

value: Columbia

tag: trangenic

value: Inducible

value: Dexamethasone


title: 183B7-25h3

description:
BiolRep2
DEX25_cuffdiff_genes.fpkm_tracking


title: Peripheral blood RNA [A584_099-2]

type: RNA

city: Oslo

first: Sjur

last: Reppe

address: Kirkeveien 166

department: Medical biochemistry

country: Norway

institute: OSLO UNIVERSITY HOSPITAL

hyb_protocol: Labeled and fragmented single stranded cDNAs were hybridized to Human Exon 1.0 ST  Arrays (Affymetrix, GPL28228). The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA, USA). The scanned images were processed using AGCC (AffymetrixGeneChip Command Console) software.

data_processing: For statistical analysis the Affymetrix.CEL files (containing probe intensities) were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). Robust microarray analysis (RMA) yielding normalized log2 transformed signal intensities were applied for normalization (http://bip.weizmann.ac.il/toolbox/overview/Partek_Users_Guide.pdf).

label: biotin

organism: Homo sapiens

source_name: Postmenopausal woman

label_protocol: 100 ng of total RNA from each sample was subjected to GeneChip WT Reagent Kit and WT Labeling Kit, following the manufacturer’s protocol for whole genome gene expression analysis (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Not Applicable

treatment_protocol: Not applicable

tag: age (years)


title: Peripheral blood RNA [A584_092]


title: V65

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
Raw reads were trimmed by fastp (version 0.20.0)
Cleaned reads were then aligned onto the human reference genome (assembly GRCh-38) using the ultrafast STAR program (version 2.5.2b)
Gene quantification was carried out using Salmon (version 0.14.1)
Assembly: GRCh-38
Supplementary files format and content: tab delimited text file with normalized transcripts per million for each sample by column and genes by row

source_name: Melanoma cell culture

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Mini kit
RNA-seq-poly-A

tag: mutation

value: BRAF

value: After Immunotherapy

tag: cell type

value: melanoma


title: V68

value: Double


title: Peripheral blood RNA [A584_097]


title: Peripheral blood RNA [A584_106]


title: V64


title: Peripheral blood RNA [A584_098-2]


title: Peripheral blood RNA [A584_089]


title: Peripheral blood RNA [A584_102]


title: Dox  rep1

description: 7-day-old seedlings


title: Peripheral blood RNA [A584_085]


title: Peripheral blood RNA [A584_088]


title: Peripheral blood RNA [A584_084]


title: EB  rep2

description: 7-day-old seedlings

value: seedling treated with EtBr


title: Peripheral blood RNA [A584_087]


title: Peripheral blood RNA [A584_093]


title: V66


title: Peripheral blood RNA [A584_091]


title: Peripheral blood RNA [A584_090]


title: V70


title: Peripheral blood RNA [A584_094]


title: Peripheral blood RNA [A584_080]


title: Peripheral blood RNA [A584_086]


title: V60

value: NRAS


title: Peripheral blood RNA [A584_078]


title: Peripheral blood RNA [A584_079]


title: ktn1-seedling-r2.fastq.gz

city: Riverside

first: Xuemei

last: Chen

state: CALIFORNIA

address: 900 University AVe

institute: University of California

data_processing:
Raw reads were subjected to adapter trimming using cutadapt. Reads without an adapter or shorter than 18-nt after trimming were discarded from further processing.
Trimmed reads were aligned to the Arabidopsis genome using ShortStack v3.8 with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were separated by size and normalization was performed by calculating the RPM (Reads per million).
The miRNAs are annotated based on Araport11.
Genome_build: TAIR 10
Supplementary_files_format_and_content: CSV file containing normalized read counts for all the annotated miRNAs.

source_name: Seedling

growth_protocol: 16 hr light and 6 hr dark on 1/2 MS medium

extract_protocol:
9-day-old Arabidopsis roots of EN7::GFP-AGO1 and ACL5::GFP-AGO1 transgenic lines in WT and ktn1-20 backgrounds were collected and ground into powder in liquid nitrogen and subjected to immunoprecipitation using GFP-Trap_MA. 14-day-old seedlings were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent.
Small RNA library construction using NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300).

value: Seedling

tag: transgene

tag: molecule subtype

value: total sRNA


title: Dox  rep2

description: 7-day-old seedlings


title: Peripheral blood RNA [A584_075]


title: Peripheral blood RNA [A584_073]


title: V63


title: V58


title: Peripheral blood RNA [A584_081]


title: V59

value: WT


title: CK  rep3

description: 7-day-old seedlings

value: seedling trested with H2O


title: Peripheral blood RNA [A584_072]


title: V57


title: CK  rep2

description: 7-day-old seedlings

value: Total seedling


title: V61

value: Unknown


title: Peripheral blood RNA [A584_071]


title: V62


title: V56

value: After Targeted Therapy


title: Peripheral blood RNA [A584_077]


title: Peripheral blood RNA [A584_076]


title: EN7-GFP-AGO1-ktn1-r1

source_name: Root

value: Root

value: AGO1-bound sRNA


title: V55


title: V54

value: After Chemotherapy


title: Peripheral blood RNA [A584_082]


title: Peripheral blood RNA [A584_074]


title: Peripheral blood RNA [A584_061]


title: EN7-GFP-AGO1-WT-r1


title: Peripheral blood RNA [A584_063]


title: V52


title: Peripheral blood RNA [A584_059]


title: ktn1-seedling-r1.fastq.gz


title: ACL5-GFP-AGO1-ktn1-r2


title: WT-seedling-r2.fastq.gz


title: CK  rep1

description: 7-day-old seedlings

value: wild type (Col-0)


title: ACL5-GFP-AGO1-ktn1-r1


title: WT-seedling-r1.fastq.gz


title: V50

value: BRAF


title: EN7-GFP-AGO1-ktn1-r2


title: Peripheral blood RNA [A584_067]


title: V53


title: Peripheral blood RNA [A584_083]


title: ACL5-GFP-AGO1-WT-r1


title: V48


title: Peripheral blood RNA [A584_068]


title: Peripheral blood RNA [A584_057]


title: Peripheral blood RNA [A584_056-2]


title: EN7-GFP-AGO1-WT-r2


title: V51

value: After Immunotherapy


title: Peripheral blood RNA [A584_062]


title: Peripheral blood RNA [A584_051]


title: Peripheral blood RNA [A584_070]


title: Peripheral blood RNA [A584_064]


title: Peripheral blood RNA [A584_069]


title: Peripheral blood RNA [A584_060]


title: Peripheral blood RNA [A584_052]


title: Peripheral blood RNA [A584_065]


title: Peripheral blood RNA [A584_066]


title: Peripheral blood RNA [A584_058]


title: V45

value: melanoma


title: Peripheral blood RNA [A584_049]


title: V49


title: Peripheral blood RNA [A584_047]


title: ACL5-GFP-AGO1-WT-r2


title: Peripheral blood RNA [A584_053]


title: V47


title: Peripheral blood RNA [A584_044]


title: Peripheral blood RNA [A584_046]


title: HET_H3K27ac_acetate

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

library_source: genomic

data_processing:
RNA-seq reads were aligned to the GRCm38 genome assembly using g Salmon (v.1.1.0) using default parameters.Expression calculations and differential gene expression analysis were excuted by tximport (v1.14.2) and DESeq2 (v1.26.0)  respectively.
DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp. After trimming with trimmomatic (v.0.36), high-quality reads were mapped to mm10 genome with bowtie 2(v2.4.1) using default parameters.Peaks were called with macs2 with default parameters relative to input sample.Manorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data
Assembly: GRCm38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: forebrain

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 53bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 6’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

tag: strain

value: forebrain

tag: age

value: post natal day 28

tag: chip antibody

value: H3K27ac(ChIP grade,ab4729,abcam)


title: Peripheral blood RNA [A584_054]


title: Peripheral blood RNA [A584_050]


title: Peripheral blood RNA [A584_042]


title: HET_input_acetate

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 57bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 10’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: Peripheral blood RNA [A584_043]


title: Peripheral blood RNA [A584_048]


title: Peripheral blood RNA [A584_039-2]


title: Peripheral blood RNA [A584_040-2]


title: Peripheral blood RNA [A584_041]


title: V44


title: Peripheral blood RNA [A584_036-2]


title: WT_H3K27ac

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: WT_input_acetate

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 55bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 8’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: V39


title: V38

value: After multiple


title: V43


title: Wt-2

molecule: polyA RNA

source_name: neuron

extract_protocol:
We firstly crossed Tdfl/fl;Nex-Cre mice with Stop-tdtomato-stop to get Tdfl/+;Nex-Cre mice to distinguish excitatory neurons with Td (Fig.5a). The Td+ cell population from forebrain of P28 was isolated through fluorescence-activated cell sorting (FACS). We performed RNA sequencing (RNA-seq) of these Td+ cells.  RNA was harvested using Trizol reagent.RNA-seq libraries from WT and Arid1a+/-  at 28-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6001 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: excitory neuron in forebrain


title: Peripheral blood RNA [A584_045]


title: V42


title: HET_H3K27ac

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 52bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 5’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: HET_input

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 56bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 9’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: Peripheral blood RNA [A584_030]


title: Peripheral blood RNA [A584_038-2]


title: Peripheral blood RNA [A584_027]


title: WT_H3K27ac_acetate

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 51bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 4’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

value: WT


title: WT_input

extract_protocol:
Freshly  forebrain tissues isolated from of WT and Arid1a+/-mice. Fixed ,Lysates,sonicated ,incubated with antibodies,cross-linking . DNA was extracted and resuspended in nuclease-free water.DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 54bp.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 7’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: V46


title: V41

value: NRAS


title: V36


title: Peripheral blood RNA [A584_055-2]


title: Peripheral blood RNA [A584_025]


title: V35


title: V40


title: Peripheral blood RNA [A584_029]


title: Peripheral blood RNA [A584_035-2]


title: V33

value: During Targeted Therapy


title: Peripheral blood RNA [A584_024]


title: Peripheral blood RNA [A584_033]


title: Peripheral blood RNA [A584_022]


title: Peptide_3

city: Nanjing

first: Ruiwei

last: Jiang

address: No.321 Zhongshan Road

department: Drum Tower Hospital Affiliated to Medical School

institute: Nanjing University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default
Assembly: mm10
Supplementary files format and content: Rawcount values for each Sample

source_name: uterus

extract_protocol:
Total RNA was isolated from the mice oviducts following the standard TRIzol extraction protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: model

value: delayed embryo implantation mouse model

value: Peptide-pThr363 derived from Nur77


title: Het-1

extract_protocol:
We firstly crossed Arid1afl/+;Nex-Cre mice with Stop-tdtomato-stop to get Arid1afl/+;Nex-Cre;Td mice to distinguish excitatory neurons with Td (Fig.5a). The Td+ cell population from forebrain of P28 was isolated through fluorescence-activated cell sorting (FACS). We performed RNA sequencing (RNA-seq) of these Td+ cells.  RNA was harvested using Trizol reagent.RNA-seq libraries from WT and Arid1a+/-  at 28-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6002 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols


title: V37


title: Peripheral blood RNA [A584_020]


title: Peripheral blood RNA [A584_032]


title: Peripheral blood RNA [A584_019]


title: Peripheral blood RNA [A584_034]


title: Peripheral blood RNA [A584_031]


title: Wt-1

extract_protocol:
We firstly crossed Tdfl/fl;Nex-Cre mice with Stop-tdtomato-stop to get Tdfl/+;Nex-Cre mice to distinguish excitatory neurons with Td (Fig.5a). The Td+ cell population from forebrain of P28 was isolated through fluorescence-activated cell sorting (FACS). We performed RNA sequencing (RNA-seq) of these Td+ cells.  RNA was harvested using Trizol reagent.RNA-seq libraries from WT and Arid1a+/-  at 28-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Peptide_2


title: Saline_3

value: Saline


title: Peripheral blood RNA [A584_037-2]

extract_protocol: RNA from whole blood was isolated according to the PAXgene Blood RNA Kit manufacturer (BD, Franklin Lakes, NJ, USA), including the optional on-column DNase digestion according to manufacturer’s instructions.


title: Peripheral blood RNA [A584_023]


title: Peripheral blood RNA [A584_015]


title: Peripheral blood RNA [A584_026]


title: Peptide_1


title: Saline_1


title: V34

value: After Targeted Therapy


title: V29

value: GNAQ


title: Fibroblast-like synoviocytes, Input DNA

city: Atlanta

first: Sergio

last: Ramirez-Perez

state: Georgia

address: 615 Michael St NE

department: Orthopaedics

institute: Emory University

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Strand NGS v4.0
peaks were called using MACS2 on Strand NGS v4.0 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3) in comparison to the input samples
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: Fibroblast-like synoviocytes

extract_protocol:
mouse FLS containing 40 million cells in each replicate were treated with or without 10ng/mL TNF for 16 h, followed by fixation with 1.5% paraformaldehyde. Chromatin was extracted and sheared into 100- to 500-bp fragments using a Diagenode Bioruptor.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 15 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 2500 following the manufacturer's protocols.

value: Fibroblast-like synoviocytes

value: untreated


title: Fibroblast-like synoviocytes, RelA ChIP

value: NF-κB p65 chip (Active Motif, Catalog No:39369, lot 11219001)


title: Peripheral blood RNA [A584_013]


title: Peripheral blood RNA [A584_012]


title: Peripheral blood RNA [A584_008]


title: Fibroblast-like synoviocytes, Sox4 - TNF ChIP

value: SOX4 (Diagenode, Catalog No:C15310129, lot A574-004)

value: TNF for 16 hours


title: Peripheral blood RNA [A584_021]


title: Saline_2


title: Peripheral blood RNA [A584_007]


title: V25

value: melanoma


title: Peripheral blood RNA [A584_017]


title: V30

value: BRAF


title: Peripheral blood RNA [A584_018]


title: Peripheral blood RNA [A584_004]


title: V28


title: V27

value: During Immunotherapy


title: V31


title: Peripheral blood RNA [A584_009]


title: Fibroblast-like synoviocytes, RelA - TNF ChIP


title: Peripheral blood RNA [A584_014]


title: V32

value: After Immunotherapy


title: Peripheral blood RNA [A584_005]


title: Peripheral blood RNA [A584_006]


title: V26


title: Peripheral blood RNA [A584_016]


title: Peripheral blood RNA [A584_010]


title: LPS_m6A_IP

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Library strategy: meRIP-seq
Illumina bcl2fastq software used for base-calling
reads algined to corresponding genomes (hg19 for human and mm9 for mouse) using TopHat (stranded), converted to sorted BAM using SAMTools, and further processed using exomePeak
gene count measurements were obtained using HTSeq-count
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: monocyte/macrophage-like cells

growth_protocol: Cells are maintained in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum  at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA were extraction follows TRI reagent protocol (Thermo-Fisher) and then treated with DNase I to remove DNA contamination. . For m6A MeRIP-seq, the m6A enrichment were performed using m6A antibody (m6A antibody cat#202203, synaptic systems) and m6A-enriched and fragmented RNA was purified using RNeasy Mini Kit as IP.
KAPA Stranded RNA-seq Kit (Illumina) was used for the library preparation of both m6A-IP RNA and input mRNAs. The quality of the completed libraries was performed with Agilent 2100 Bioanalyzer

treatment_protocol: RAW264.7 cells at 4×10^5 cells per mL were treated with LPS at 10 ng/mL and harvested at 6 h post treatment. HeLa cells were infected with HSV1 at 5 MOIs and harvested at 5 or 8 h post-infection

tag: cell line

value: 6hr LPS treatment

tag: rna harvest

value: Enrichment of m6A methylated mRNA with m6A antibody (Abcam, ab208577)


title: no_LPS_m6A_IP

value: Control/no LPS treatment


title: Fibroblast-like synoviocytes, Sox4 ChIP


title: no_LPS_Input

value: Input RNA


title: LPS_Input

value: 6hr after LPS treatment


title: Peripheral blood RNA [A584_002]


title: Peripheral blood RNA [A584_003]


title: Peripheral blood RNA [A584_001]


title: V22

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Mini kit
RNA-seq-poly-A


title: 2.-Esrrb_ miRNA_Day 1

city: Barcelona

first: Ana

last: Sevilla

state: ESP

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

country: Spain

institute: Universidad de Barcelona

description: Day 1 (+D0X) Esrrb expressed

data_processing:
none provided by the submitter
Genome_build: mm9

source_name: Mouse ES_AINV15

growth_protocol: For all experiments,Esrrb_R clone was grown on irradiated MEFS   in mESC media ( D-MEM–High Glucose (Dulbecco’s modified Eagle’s medium-1X-High Glucose) (Gibco®, Invitrogen), 15% FBS (Fetal bovine serum) (Hyclone, Thermo Scientific), 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, Penicillin/Streptomycin (Gibco, Invitrogen) and 103 U/ml LIF (Chemicon, Millipore). All cell cultures were maintained at 37ºC with 5% CO2.

extract_protocol:
Short transcript libraries were generated using size selected RNA. Total RNA at different time points after downregulation of Esrrb was extracted with Qiazol® (Qiagen) with subsequent enrichment for small RNAs (<200 bp) using the miRNeasy® Mini purification kit according to the manufacturers’ instructions for total RNA isolation that includes the small fraction. Extracted RNA (40 µg) was combined with trace amounts of 5´-32P-labeled RNA standards, 19-nt 5’-CGUACGCGGGUUUAAACGA-3’ and 24-nt 5’-CGUACGCGGAAUAGUUUAAACUGU-3'. RNA was then fractionated on a 15% polyacrylamide, 8 M urea gel (Bio-Rad).  A gel fragment spanning both the 18 nt and 24-26 nt internal standards was excised, and RNA was eluted and ethanol-precipitated in siliconized tubes, with 20 µg of glycogen as carrier. Gel-purified 18-26 nt RNA was incubated with 50 µM pre-adenylylated 3´-adaptor oligonucleotide (Modban), 10X ATP-free ligase Buffer (500 mM Tri-HCl (pH=7.5-7.6), 100 mM MgCl2, 100mM DTT, 600 µg/ml BSA), and T4 RNA Ligase 2, truncated (New England BioLabs) in a 20 µl reaction at 37°C for 1 hour. The T4 RNA ligase reaction was purified on a 15% polyacrylamide, 8 M urea gel (Bio-Rad) by using the ligated forms of the standards as a guide for band excision. RNAs ligated with 3´-adaptor oligonucleotide was eluted and ethanol-precipitated in siliconized tubes, with 20 µg of glycogen. Ligated RNA product was used in a second T4 RNA ligase reaction for the 5’-adaptor oligonucleotide (Solexa Linker). Ligated products were gel-purified, excising the gel fragment spanning the doubly ligated standards. Gel-purified doubly ligated RNA was used in a standard 20µl RT reaction (SuperScript III, Invitrogen) with the RT primer, ATTGATGGTGCCTACAG (BanOne). The cDNA was PCR amplified with the 5’and 3’primers, generating products with an extended 3’ adaptor sequence. PCR products were digested with Pme I (NEB) at 37ºC for 3 hours. DNA fragments ranging from 108-113 bp were isolated from a low-melting point agarose gel. After further phenol extraction and ethanol precipitation, DNA samples were resuspended in Elution buffer (10 mM Tris/0.1% Tween) and then used according to the standard Solexa sequencing protocol (Illumina). Each library was run on one lane of the Solexa sequencer at the Genomic Sequencing Core at Icahn School of Medicine at Mount Sinai.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Esrrb_R rescue clone was grown in +Dox (1ug/ml) media_Day0; Dox withdrawal was performed for 5 days performing  miRNA-Seq at the respective days: Day0 ( Esrrb expressed) and days  1,3 and 5 ( Esrrb non expressed)

tag: sample type

value: Esrrb_ Recue clone

value: -Dox


title: 3.-Esrrb_ miRNA_Day 3

description: Day 3 (+D0X) Esrrb expressed


title: V24

value: NRAS


title: Esrrb_R_day5_-Dox_rep2

description: 1_Exiqon*.txt and 0_Exiqon*.txt contain raw data from ch1 (Hy3) and ch2 (Hy5) sample, respectively.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing: The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 - Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Values that should be disregarded (e.g., failed, not detected') are labeled as "null".

label_protocol: 1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: A murine ESC line with controllable Esrrb expression (Esrrb_R) was maintained on irradiated primary mouse embryonic fibroblasts (MEFs). For all experiments, ESCs were cultured on 0.1% gelatin-coated tissue culture plates without feeder cells. Esrrb_R cell line was maintained in media containing  Glucose (Dulbecco’s modified Eagle’s medium-1X-High Glucose) (Gibco®, Invitrogen), 15% FBS (Fetal bovine serum) (Hyclone, Thermo Scientific), 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, Penicillin/Streptomycin (Gibco, Invitrogen) and 103 U ml-1 LIF (Chemicon, Millipore) and Doxycycline (Dox) (1 µg ml-1, Sigma) D-MEM-High . All cell cultures were maintained at 37C with 5% CO2 and cells were plated at a density of 3×10^5 cells per 10 cm dish.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: To induce differentiation, we withdrew Doxycycline (Dox) (1 µg ml-1, Sigma) from the media while maintaining all other routine ESC nutrients and harvested cells at Day1, Day3 and Day5

tag: dox withdrawal

source_name: Common Reference Pool

value: reference (pool of Esrrb Day0 + Day 1 samples)


title: 4.-Esrrb_ miRNA_Day 5

description: Day 5 (+D0X) Esrrb expressed


title: V21

value: After Targeted Therapy


title: Esrrb_R_day5_-Dox_rep1

value: murine ESC line with controllable Esrrb expression (Esrrb_R)


title: Esrrb_R_day5_-Dox_rep3


title: Esrrb_R_day3_-Dox_rep2


title: Esrrb_R_day3_-Dox_rep3


title: V20


title: V23


title: bacteria_4h_Elution_1, repeat 2

data_processing:
Library strategy: meRIP-seq
Illumina bcl2fastq software used for base-calling
reads algined to corresponding genomes (UCSC mm9 for mouse) using TopHat (stranded), converted to sorted BAM using SAMTools, and further processed using exomePeak
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

growth_protocol: RAW 264.7 Cells are maintained in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum  at 37 °C in a humidified atmosphere with 5% CO2.

treatment_protocol: RAW264.7 cells at 4×10^5 cells per mL were infected with 107 P.aeruginosa and harvested at 0, 2, 4, and 6 h post treatment. RAW264.7 cells with ALKBH5 knockdown (ALKBH5 si1: SASI_Mm01_00106232, ALKBH5 si2: SASI_Mm02_00344968, Sigma-Aldrich) were infected with 107 P. aeruginosa 6 hr post infection.

value: P.aeruginosa infection 4h


title: bacteria_4h_Input_1, repeat 2


title: bacteria_6h_Elution_1, repeat 2

value: P.aeruginosa infection 6h


title: Esrrb_R_day1_-Dox_rep3


title: bacteria_2h_Input_1, repeat 2

value: P.aeruginosa infection 2h


title: Esrrb_R_day3_-Dox_rep1


title: bacteria_2h_Elution_1, repeat 2


title: V19

value: BRAF

value: melanoma


title: Peripheral blood RNA [A584_011]


title: V16

value: During Targeted Therapy


title: Het-2

extract_protocol:
We firstly crossed Arid1afl/+;Nex-Cre mice with Stop-tdtomato-stop to get Arid1afl/+;Nex-Cre;Td mice to distinguish excitatory neurons with Td (Fig.5a). The Td+ cell population from forebrain of P28 was isolated through fluorescence-activated cell sorting (FACS). We performed RNA sequencing (RNA-seq) of these Td+ cells.  RNA was harvested using Trizol reagent.RNA-seq libraries from WT and Arid1a+/-  at 28-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6003 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: excitory neuron in forebrain

value: post natal day 28

tag: genotype


title: V18

value: cKIT

tag: treatment


title: bacteria_6h_Elution_1, repeat 1

value: Enrichment of m6A methylated mRNA with m6A antibody (Abcam, ab208577)


title: 1.-Esrrb_miRNA_ Day 0

description: Day 0 (+D0X) Esrrb expressed

value: +Dox


title: bacteria_0h_Elution_1, repeat 1

value: P.aeruginosa infection 0h


title: bacteria_0h_Elution_1, repeat 2


title: V17

value: After Immunotherapy


title: bacteria_6h_Input_1, repeat 1

value: Input RNA


title: bacteria_4h_Input_1, repeat 1


title: Esrrb_R_day1_-Dox_rep2

value: reference (pool of Esrrb Day0 + Day 1 samples)


title: HEK293T_input

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Basecalls performed using illumina bcl2fastq2.
Adapters were trimmed with cutadapt (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --max-n 0 -e 0.1 -q 20 -m 20 --trim-n)
Cleaned reads were mapped to genome and transcripome with hisat2 (--rna-strandness R). Only unique alignments were used.
BAM was converted to bedGraph by bedtools
Winscores (enrichment) of 50 nt windows in transcriptome were computed by customized script.
Assembly: hg38
Supplementary files format and content: Alignment records in bedGraph and computed winscores in bed

extract_protocol:
Total RNA was isolated from tissues using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
RNA samples were fragmented in 1X NEB Next Magnesium RNA Fragmentation Buffer at 94℃ for 5min and fragmented RNA was then cleaned up using ethanol precipitation. 10ng fragmented RNA was used to construct input control library with VAHTS stranded mRNA-seq library prep kit (Vazyme). 15-40ug fragmented RNA was further incubated with 5ug rabbit anti-m6A polyclonal antibody (Synaptic Systems, catalog number 202003) in IPP buffer overnight at 4℃. The m6A-Ab mixture was then immunoprecipitated by incubation with protein-G magnetic beads at 4℃ for another 2h. After washing with IPP buffer, bound RNA was competitively eluted from the beads with 0.5mgml-1 N6-methyladenosine (Sigma-Aldrich), followed by ethanol precipitation. RNA was resuspended in 8μl water and used for library construction.

tag: experiment

value: Input


title: V14


title: bacteria_0h_Input_1, repeat 1


title: Esrrb_R_day1_-Dox_rep1

value: murine ESC line with controllable Esrrb expression (Esrrb_R)


title: Esrrb_R_day0_+Dox_rep3


title: bacteria_6h_Input_1, repeat 2


title: V11

value: NRAS


title: V15

value: WT


title: HEK293T_IP

value: IP


title: bacteria_2h_Input_1, repeat 1

value: P.aeruginosa infection 2h


title: Esrrb_R_day0_+Dox_rep2


title: V10

value: melanoma


title: si2_ALKBH5_input, repeat 1

value: ALKBH5 knockdown si2 followed by P.aeruginosa infection 6h


title: V13

value: Double


title: bacteria_0h_Input_1, repeat 2


title: V12

value: BRAF


title: si2_ALKBH5_elution, repeat 1


title: bacteria_4h_Elution_1, repeat 1

value: P.aeruginosa infection 4h


title: si2_ALKBH5_elution, repeat 2

value: Enrichment of m6A methylated mRNA with m6A antibody (Abcam, ab208577)


title: si1_ALKBH5_elution, repeat 1

value: ALKBH5 knockdown si1 followed by P.aeruginosa infection 6h


title: si2_ALKBH5_input, repeat 2


title: M1E07122016

city: Boston

first: Ionita

middle: Calin

last: Ghiran

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
Plasma samples were obtained from 3 (M1-M3) male and 3 female (F1-F3) healthy individuals; 4 anticoagulants (E-EDTA, H-Heparin, C-Citrate, R-hiRudin) were used to collect plasma. RNA Isolation kit was Serum and Plasma kit (Qiagen).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were not multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

tag: Sex

value: male

tag: tissue

value: plasma

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Serum and Plasma kit (Qiagen)


title: M1R07122016


title: V9

tag: mutation

value: cKIT

tag: cell type


title: M1C07122016


title: si1_ALKBH5_input, repeat 1

value: Input RNA


title: si1_ALKBH5_elution, repeat 2


title: si1_ALKBH5_input, repeat 2


title: Esrrb_R_day0_+Dox_rep1

value: murine ESC line with controllable Esrrb expression (Esrrb_R)

value: reference (pool of Esrrb Day0 + Day 1 samples)


title: NC_elution, repeat 2

value: ALKBH5 knockdown negative control followed by P.aeruginosa infection 6h


title: bacteria_2h_Elution_1, repeat 1

value: P.aeruginosa infection 2h


title: NC_elution, repeat 1


title: V7

value: NRAS

value: melanoma


title: M2E07122016


title: M2R07122016


title: Female_H3K79me2_Rep2

city: ROSCOFF

first: Olivier

last: GODFROY

address: Place Georges Teissier CS90074

department: Station Biologique de Roscoff

country: France

institute: CNRS

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Cutadapt (Hansen et al., 2016)
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (Langmead et al., 2009) and duplicates were removed using samtools markdup (v 1.9 - Li et al., 2009).
H3K79me2 was analysed using SICER (v1.1) (minimum FDR of 0.01) (Xu et al., 2014; Zang et al., 2009) with a window size of 200 bp and a gap size of 400 bp. The signal was normalized using the Signal Extraction Scaling (SES) method (Diaz et al., 2012).
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.

organism: Ectocarpus sp. Ec460

growth_protocol: Cultures were grown in 140 mm round Petri dishes in natural sea water with 0.01% Provasoli enrichment at 13°C with a 12h/12h day/night cycle and 20 (µmol photons).m-2.s-1 irradiance.

extract_protocol:
For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 1% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM potassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without 1% triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 200mM NaCl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For RNA-seq, RNA was extracted from the same duplicate male and female gametophytes cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA concentration have been assessed using a Qubit 2.0 Fluorometer (Thermofisher). RNA contamination for genomic DNA have been tested by PCR using pairs of primers specific to the non-coding genome.
Illumina librairies corresponding to “NAR_” files were prepared and sequenced in the Genome Center of the Max Planck Institute for Developmental Biology (Tuebingen, Germany)  using the TruSeq ChIP-seq.

treatment_protocol: No treatment

value: Female

value: whole organism

tag: Stage

value: mature, 4 weeks old

tag: phenotype

value: imm

tag: chip antibody

value: Di-Methyl-Histone H3 (Lys79) (D15E8) XP Rabbit mAb, CST, lot 5427


title: NC_input, repeat 1

tag: cell line

tag: rna harvest


title: Female_H3K79me2_Rep1


title: V8


title: V5

value: BRAF


title: NC_input, repeat 2


title: V6


title: F2C07122016

value: Healthy Subject

value: female

value: plasma

value: Entire cardiovascular system


title: Female_H3_Rep2_2

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST #4620 Lot No 12


title: Female_Input_Rep1_2

value: none (input)


title: Female_Input_Rep2_2


title: Female_H4K20me3_Rep2

description:
Corresponding replicate: ADPH-44
Female_ChIP_H4K20me3_inputH3_subtract.bdg.bw
Female_ChIP_H4K20me3_SICER

data_processing:
Illumina base calling
Sequence quality was evaluated with FASTQC and poor quality sequence removed with Cutadapt (Hansen et al., 2016)
ChIP-seq Illumina reads were mapped onto the Ectocarpus genome using Bowtie (Langmead et al., 2009) and duplicates were removed using samtools markdup (v 1.9 - Li et al., 2009).
Peaks corresponding to regions enriched in H3K4me3, H3K9ac and H3K27ac were identified using the MACS2 (version 2.1.1) callpeak module (minimum FDR of 0.01) and refined with the MACS2 bdgpeakcall and bdgbroadcall modules (Zhang et al., 2008). H3K36me3 and H4K20me3 were analysed using SICER (v1.1) (minimum FDR of 0.01) (Xu et al., 2014; Zang et al., 2009) with a window size of 200 bp and a gap size of 400 bp. The signal was normalized using the Signal Extraction Scaling (SES) method (Diaz et al., 2012).
RNAseq reads were trimmed and filtered using Cutadapt (Martin, 2011) with a quality threshold of 33 (quality-cutoff) and a minimal size of 30 bp. Then filtered reads were mapped to version v2 of the Ectocarpus sp. genome (Cormier et al., 2017a) using TopHat2 with the Bowtie2 aligner (Kim et al., 2013).
Mapped RNA-seq data was processed with featureCounts (Liao et al., 2014) to obtain counts of numbers of reads mapped to exons. Expression values were represented as TPM.
Differential expression was detected using the DESeq2 package (Bioconductor; Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550) using an adjusted p‐value cut‐off of 0.05 and a minimal fold‐change of 2.
Genome_build: Ectocarpus sp. Ec32 genome v2 2018 (https://bioinformatics.psb.ugent.be/orcae/overview/EctsiV2)
Supplementary_files_format_and_content: bigWig files were generated from bam files, which were merges of the two replicates, normalised with SES with the signal subtract from the input using deeptools (v3.2.0; Fidel R, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. 2016. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research 44:W160-W165). Peak calling files, based on the bigWig files, are in either narrowPeak (bed9) or broadPeak (bed12) format.

extract_protocol:
For ChIP-seq, Ectocarpus tissue was fixed for five minutes in seawater containing 1% formaldehyde and the formaldehyde eliminated by rapid filtering followed by incubation in PBS containing 400 mM glycine. Nuclei were isolated by grinding in liquid nitrogen and in a Tenbroeck Potter in nuclei isolation buffer (0.1% triton X-100, 125 mM sorbitol, 20 mM potassium citrate, 30 mM MgCl2, 5 mM EDTA, 5 mM β-mercaptoethanol 55 mM HEPES at pH 7.5 with complete ultra protease inhibitors), filtering through Miracloth and then washing the precipitated nuclei in nuclei isolation buffer with and then without 1% triton X-100. Chromatin was fragmented by sonicating the purified nuclei in nuclei lysis buffer (10 mM EDTA, 1% SDS, 50 mM Tris-HCl at pH 8 with complete ultra protease inhibitors) in a Covaris M220 Focused-ultrasonicator (duty 25%, peak power 75, cycles/burst 200, duration 900 sec at 6°C). The chromatin was incubated with an anti-histone PTM antibody overnight at 4°C and the immunoprecipitation carried out using Dynabeads protein A and Dynabeads protein G. Following immunoprecipitation and washing, a reverse cross-linking step was carried out by incubating for at least six hours at 65°C in 200mM NaCl and the samples were then digested with Proteinase K and RNAse A. The purified DNA was then prepared for Illumina sequencing. For RNA-seq, RNA was extracted from the same duplicate male and female gametophytes cultures as were used for the ChIP-seq analysis using the Qiagen RNeasy plant mini kit with an on-column Deoxyribonuclease I treatment. RNA concentration have been assessed using a Qubit 2.0 Fluorometer (Thermofisher). RNA contamination for genomic DNA have been tested by PCR using pairs of primers specific to the non-coding genome.
Illumina librairies were prepared by Fasteris using the TruSeq ChIP-seq (for ChIP-seq) or TruSeq RNA stranded protocol (for RNA-seq) before sequencing.

value: Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb, CST #5737

tag: sample code


title: Female_H3_Rep1_2


title: V4


title: V3


title: M2C07122016

value: male

value: total cell-free biofluid RNA

value: Serum and Plasma kit (Qiagen)


title: F3C07122016


title: Female_H3K9ac_Rep1

description:
Corresponding replicate: ADPH-60
Female_ChIP_H3K9ac_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K9ac_MACS2

value: Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb, CST #9649 Lot No 0011


title: Female_H4K20me3_Rep1

description:
Corresponding replicate: ADPH-45
Female_ChIP_H4K20me3_inputH3_subtract.bdg.bw
Female_ChIP_H4K20me3_SICER

value: Female


title: M3C07122016


title: V2

value: cKIT

value: melanoma


title: Female_H3K9ac_Rep2

description:
Corresponding replicate: ADPH-59
Female_ChIP_H3K9ac_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K9ac_MACS2

value: whole organism

value: mature, 4 weeks old

value: imm


title: M3E07122016

value: Healthy Subject


title: F1R07122016

value: female


title: Female_H3K4me3_Rep1

description:
Corresponding replicate: ADPH-57
Female_ChIP_H3K4me3_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K4me3_MACS2

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb, CST #9751Lot No 0009


title: Female_H3K4me3_Rep2

description:
Corresponding replicate: ADPH-56
Female_ChIP_H3K4me3_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K4me3_MACS2


title: V1

value: NRAS


title: Female_H3K36me3_Rep1

description:
Corresponding replicate: ADPH-40
Female_ChIP_H3K36me3_inputH3_subtract.bdg.bw
Female_ChIP_H3K36me3_SICER

value: Anti-Histone H3 (tri methyl K36) antibody, Abcam ab9050


title: Female_H3K36me3_Rep2

description:
Corresponding replicate: ADPH-39
Female_ChIP_H3K36me3_inputH3_subtract.bdg.bw
Female_ChIP_H3K36me3_SICER


title: Female_H3K27ac_Rep2

description:
Corresponding replicate: ADPH-61
Female_ChIP_H3K27ac_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K27ac_MACS2

value: Anti-acetyl-Histone H3 (Lys27) Antibody, Millipore 07-360 Lot No 2987402


title: H3K9me3_Ad-D3-rep2 [re-analysis]

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo

description: re-analysis of GSM3394768

data_processing:
ChIP-seq and RNAseq reads were aligned to the hg38 reference genome using bowtie2 version 2.4.1 for ChIP-seq reads and BWA-MEM version 0.7.12  for RNAseq reads
Duplicate reads were removed using picard MarkDuplicates
For RNA-seq,  reads per transcript were counted using featureCounts from Subread package 2.0.1. Differential gene expression was determined using DESeq2 1.30.0.
For histone modification ChIPseq, H3K4me1 peaks were called from both replicated using macs2 2.2.7.1 .
For LMNB1 ChIPseq, Peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: featureCounts.txt : tab-delimited text files with 2 columns: transcript ID , read count
Supplementary_files_format_and_content: DESeq2_counts.txt :  tab-delimited text files with 2 columns: transcript ID , DESeq2 normalized count
Supplementary_files_format_and_content: bed files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: Bigwig file with log2ratio ChIP/Input were generated using bamCompare from deeptools 3.5.1.

source_name: Human primary adipose stem cells

growth_protocol: Human normal ASCs purifed from adipose tissue were cultured in proliferating state in DMEM/F12 containing 10 % fetal calf serum and 20 ng/ml basic fibroblast growth factor.

extract_protocol:
For ChIP, cells were sonicated to produce chromatin fragments of ~200 base-pairs, lysates were clarified by sedimentation and histone-DNA or Lamin-DNA complexes were isolated from supernatants by ChIP using specific antibodies. RNA was purified from cell lysates using the RNEasy mini kit (Qiagen).
ChIP-seq and RNA-seq sequencing libraries were prepared according to  Illumina protocols for sequencing on a Nextseq500 or Novaseq (ChIP-seq) or on a Nextseq500 (RNA-seq) at the Norwegian Sequencing Center.

treatment_protocol: Proliferating cells were harvested, re-seeded at confluency and cultured confluent for 48 h without fibroblast growth factor. At T00, ASCs were induced to differentiate with 10 µg/ml insulin, 200 µM indomethacin, 1µM dexamethasone and 0.5 µM 3-isobutyl-1-methylxanthine.  Cells were collected at indicated timepoints for protein, RNA and chromatin preparations and analyses.

tag: time point

value: Day 3

value: ASCs on day 3 after adipogenic induction

value: anti-H3K9me3 antibody (Diagenode pAB-056-050, at 2.5 microgram per 5 million cells)

tag: replicate


title: H3K9me3_Ad-D1-rep2 [re-analysis]

description: re-analysis of GSM3394767

value: Day 1

value: ASCs on day 1 after adipogenic induction


title: Female_H3K27ac_Rep1

description:
Corresponding replicate: ADPH-62
Female_ChIP_H3K27ac_merge_sorted.bam.subtract.bdg.bw
Female_ChIP_H3K27ac_MACS2

value: Female


title: F2R07122016

value: plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Serum and Plasma kit (Qiagen)


title: F3R07122016


title: Female_H3_Rep2

description: Corresponding replicate: ADPH-49

value: whole organism

value: mature, 4 weeks old

value: imm

value: Histone H3 (D2B12) XP Rabbit mAb (ChIP Formulated), CST #4620 Lot No 12


title: Female_H3_Rep1

description: Corresponding replicate: ADPH-51


title: H3K9me3_D0-rep2 [re-analysis]

description: re-analysis of GSM3394766

value: Day 0

value: ASCs on the day of differentiation induction


title: H3K9me3_Ad-D3-rep1 [re-analysis]

description: re-analysis of GSM3394765


title: F3E07122016

value: Healthy Subject

value: female


title: F1E07122016


title: Female_RNA_Rep2

description: Corresponding replicate: ADPH-65


title: Female_Input_Rep2

description: Corresponding replicate: ADPH-55


title: Female_Input_Rep1

description: Corresponding replicate: ADPH-58


title: H3K9me3_Ad-D1-rep1 [re-analysis]

description: re-analysis of GSM3394764


title: Female_RNA_Rep1

description: Corresponding replicate: ADPH-66


title: H3K9me3_D0-rep1 [re-analysis]

description: re-analysis of GSM3394763


title: Control 3

city: Jinju

first: Preethi

last: Vetrivel

state: Singapore

address: Gajwa-dong

country: South Korea

institute: Gyeongsang National University

data_processing:
The paired end sequenced samples were preprocessed using Trimmomatic tool version -0.36.The trimmed seq reads were mapped to human reference genome GRCh38 (Gencode release 12)  using STAR.
The expression level of genes from RNASeq reads were identified using RSEM and the individual transcript expression was calculated.
Assembly: Human reference genome GRCh38 (Gencode release 12)
Supplementary files format and content: tab-delimited text files contains expression counts and TPM (Transcript per million) values for each sample with ensembl IDs of genes.

source_name: AGS gastric cancer cells

growth_protocol: AGS gastric cancer cells were cultured routinely and seeded at a density of 5 × 105 per well on a 60 mm plate supplemented with RPMI medium containing 10% FBS. The cells were allowed to grow by maintaining 5% Co2 at 37 °C

extract_protocol:
Cell lysates were collected and total RNA was extracted using Trizol reagent.About 1 ug of total RNA was used to generate NGS sequenicng libraries.
NGS sequencing libraries was prepared using TruSeq RNA Sample Prep kit (Illumina). The Poly-a containing RNA molecules were prurified and fragmented which are reverse transcribed into cDNA with random primers. The short fragments were purified with QiaQuick PCR extraction kit and connected with sequencing adapters and each library was separted by adjoining distinct MID tags. The resulting cDNA libraries were then paired-end sequenced (2 x 101 bp) with NovaSeq 6000 system (Illumina).

treatment_protocol: The cells were treated with flavonoid prunetin at concentrations (0 and 80) for 24 h at 37 °C

value: AGS gastric cancer cells

tag: treatment

value: Untreated


title: Test 1

value: prunetin


title: M3R07122016

tag: condition

value: male


title: D35

city: Zhanjiang

first: Yujie

last: Cai

state: Guangdong

address: Renmindadaonan 57th

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and FPKM values for each sample

source_name: Cubital vein peripheral whole blood

extract_protocol:
Use EDTA anticoagulation tube to collect  blood, aliquot it into centrifuge tube and quick-freeze it in liquid nitrogen and store it at -80℃.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: MDD patients were recruited through outpatients and inpatients in the Department of Psychology of the Affiliated Hospital of Guangdong Medical University. All MDD patients met the following inclusion criteria: (1)Met the MDD diagnostic criteria of Manual of Mental Disorders (5th Edition) (DSMV); (2) The 24-item Hamilton Depression Scale (HAMD-24) score >= 8, Self-rating depression scale (SDS) score >= 53; (3) Age 14 to 59 years, and the age of MDD onset under 55 years; (4) Han people; (5) First episode depression patients without any medications or not taking any psychiatric medication for at least three months; (6) No history of infection, no obvious physical disorder; (7) No history of smoking or alcoholism; (8) No history of head trauma. And the following exclusion criteria were applied for the MDD patients: (1) With other mental disorder, e.g., substance abuse, schizophrenia, obsessive-compulsive disorder, etc.; (2) Pregnant or lactating female; (3) Long-term use of drugs or health care products. The healthy controls were recruited in the community and the inclusion criteria were as following: (1) The 24-item Hamilton Depression Scale (HAMD-24) score < 8, Self-rating depression scale (SDS) score < 53; (2) Age 18 to 59 years; (3) Han people; (4) Not taking any medication for at least three months; (5) No history of mental disorder and no family history of major mental disorder, no significant physical disorder; (6) No history of smoking or alcohol abuse. The following exclusion criteria were applied for the healthy controls:(1) Pregnant or lactating female; (2) Long-term use of drugs or health care products. All participants were jointly diagnosed by two or more psychiatrists.

tag: disease state

value: major depressive disorder patients

value: Cubital vein peripheral whole blood


title: F1C07122016

tag: Sex

tag: tissue

value: plasma

value: Entire cardiovascular system


title: D33

institute: Affiliated Hospital of Guangdong Medical University


title: Control 1


title: D32


title: F2E07122016

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

value: Serum and Plasma kit (Qiagen)


title: Panc1 Control Drop-seq

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Single cell RNA-seq was performed using Drop-seq

data_processing:
DropSeq: Illumina Casava1.7 software used for basecalling. 10xGenomics: Fastq files from NovaSeq was processed using the function "count" (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1) in 10X Genomics Cellranger version 6.0.0 with default paramaters.
Drop-seq: Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13 using STAR as aligner. Both Drop-seq and 10x Genomics reads were aligned against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or CellRanger 6.0.0.
Drop-seq: The aligned libraries were further processed into Digital Gene Expression (DGE) matrix using the Drop-seq program DigitalExpression tool (integrated in Drop- seq_tools-1.13). The number of cells that were extracted from aligned BAM file was based on the knee plot procedure, which extracts the number of reads per cell, then plots the cumulative distribution of reads and selects the knee of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Drop-seq: Tab-delimited text file; gene expression (as count) of each gene for each extracted cell. 10x Genomics: features, barcodes and matrix as the deafult from CellRanger 6.0.0. Processed Seurat objects.
10x Genomics: features, barcodes and matrix as the deafult from CellRanger 6.0.0. Processed Seurat objects.

source_name: Panc1 untreated

growth_protocol: Panc1 cells was grown in DMEM + 10% FBS + 1% P/S (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for no more than 5 passages before collection for scRNA-seq analysis. Panc1-GR cells were grown similarly, though the culture media supplemented with 10uM Gemcitabine prior to the experiment.

extract_protocol:
Drop-seq or 10x Genomics Chromium Controller on the single cell suspension
Drop-seq: Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol). 10x Genomics: Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol: 500,000 Panc1 cells were seeded in 6 well plates in DMEM + 10% FBS + 1% P/S. After two days, the media was aspirated and replaced with 2mL of either a vehicle control (media with 2µL PBS per 2mL, PANC1CTRL) or media supplemented with 2µM Gemcitabine (2uL stock solution per 2mL, PANC1GEM24H). After 24 hours, cells were trypsinized, centrifuged, resuspended in DMEM, counted, and processed for Drop-seq. Experiments using Panc1-GR were performed similarly, though cells were treated with 10µM (2uL stock solution per 2mL) of either W-7, BAPTA-AM, or 5µM  (1uL stock solution per 2mL) Amlodipine, and processed for 10x Genomics.


title: fastATAC_VAL_8h_r2

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 East Duarte Road

department: Toni Stephenson Lymphoma Center

institute: City of Hope

description:
Replicate 2
Diff_Peak_Down_VAL_AZ4573_8h_vs_VAL_DMSO.bed

data_processing:
We followed the ATAC-seq guidelines published on Harvard FAS informatics (https://informatics.fas.harvard.edu/atac-seq-guidelines.html) to process the raw ATAC-seq fastq files. Briefly, reads were aligned to the hg19 reference genome using bowtie2 with “--very-sensitive” option. After removing mitochondrial reads, non-uniquely aligned reads, and PCR duplicates, MACS2 with parameter “-q 0.05” was used to perform peak calling for each sample. To obtain a consensus-set of peaks across samples, peak files were merged using the ‘merge’ function in bedtools. The number of reads that fell into the merged peaks was obtained using the ‘multicov’ function in bedtools, with parameters “-q 10” to exclude reads with poor mapping quality, and “-f 0.05” to exclude reads that only minimally overlap the peak. The obtained read counts for peaks were processed in DESeq2. to identify hyper- and hypo-accessible peaks across different conditions. Peaks were called hyper or hypo-accessible using the absolute fold change larger than 1.5 and adjusted p-value less than 0.01 from DESeq2.
Assembly: hg19
Supplementary files format and content: Processed data 1: bigWig of each sample. Processed data 2: bed files generated using DESeq2 for increased peaks "up" and decreased peaks "down". Replicates were used to compare 3h drug treatment versus 0h, and 8h drug treatment versus 0h in each cell line.

source_name: cultured immortalized DLBCL cells

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Samples were prepared according to the standard ATAC-seq protocol or the Fast-ATAC protocol, a method optimized for blood cells. For the Fast-ATAC, 5e4 cells were suspended in 22 µL of dPBS, and were added to 28 µL of transposase mixture (25 µL of 2x TD buffer, 2.5 µL of TDE1, 0.5 µL of 1% digitonin). The samples were incubated at 37°C for 30 minutes in a simpliamp thermocycler. DNA was purified using a DNA Clean and Concentrator-5 capped kit.
The transposed DNA fragments were amplified for paired end sequencing using custom Nextera PCR primers 1 and 2.

treatment_protocol: Cells were treated with AZD4573 (30 nM) in duplicate for 0, 3, or 8 hours.

value: VAL

tag: atac method

value: Fast-ATAC-seq (5,000 cells)

tag: treatment time

value: 8 hours


title: fastATAC_VAL_3h_r2

description:
Replicate 2
Diff_Peak_Down_VAL_AZ4573_3h_vs_VAL_DMSO.bed

value: 3 hours


title: H3K4me1_Input_T24

value: 24 Hours (T24)

tag: cell type

value: ASCs on 24 hours after adipogenic induction


title: fastATAC_VAL_3h_r1

description:
Replicate 1
Diff_Peak_Down_VAL_AZ4573_3h_vs_VAL_DMSO.bed


title: C10

value: healthy controls


title: fastATAC_OCI_LY3_8h_r2

description:
Replicate 2
Diff_Peak_Down_LY3_AZ4573_8h_vs_LY3_DMSO.bed


title: C9


title: H3K4me1_Input_T16

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction


title: C8


title: fastATAC_OCI_LY3_8h_r1

description:
Replicate 1
Diff_Peak_Down_LY3_AZ4573_8h_vs_LY3_DMSO.bed


title: fastATAC_OCI_LY3_3h_r2

description:
Replicate 2
Diff_Peak_Down_LY3_AZ4573_3h_vs_LY3_DMSO.bed


title: H3K4me1_Input_T12

value: 12 Hours (T12)

value: ASCs on 12 hours after adipogenic induction


title: fastATAC_OCI_LY3_3h_r1

description:
Replicate 1
Diff_Peak_Down_LY3_AZ4573_3h_vs_LY3_DMSO.bed


title: fastATAC_OCI_LY3_0h_r1

description: Replicate 1

value: 0 hours


title: C7

value: Cubital vein peripheral whole blood


title: Test 2

value: AGS gastric cancer cells

value: prunetin


title: Test 3


title: fastATAC_OCI_LY3_0h_r2

description: Replicate 2


title: H3K4me1_Input_T08

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction


title: ATAC_VAL_8h_r2

value: VAL

value: Standard ATAC-seq (50,000 cells)


title: H3K4me1_Input_T04

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: Control 2

value: Untreated


title: 2023Rep2Feature Barcoding

city: New Haven

first: Jack

middle: Anthony

last: Collora

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

data_processing:
Library strategy: scFeature Barcoding
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

molecule: other

source_name: CD4+ T cells

growth_protocol: Isolated resting CD4+ T cells by negative selection: no growth conditions ; antigen stimulated CD4+ T cells: RPMI with 10% human serum for 9h after antigen stimulation

extract_protocol:
10X was used for all single cell experiements following the 5' v1.1 immune profiling with feature barcoding protocol. For the bulk TCR, CD4+ T cells were isolated by negative selection, and total RNA was extracted using the Zymo Directzol RNA kit.
10X Immune Profiling V1.1. Briefly, after cDNA amplification, cDNA is separated into high molecular weight (HMW) and low molecular weight (LMW) fractions. The LMW fraction is library prepped to generate CITE-seq libraries of surface protein expression. The HMW is sheered enzymatically, end repaired, and adapters are ligated on to generate the transcriptome library. In parallel, targetted amplification of TCR sequences occurs on the HMW fraction.

treatment_protocol: Isolated resting CD4+ T cells by negative selection: no treatment protocol ; antigen stimulated CD4+ T cells: treated with antigen peptide pools for 9h in the presence of T20 fusion inhibitor, sorted using FACS ARIA for AIM+

tag: cell state

value: Isolated unstimulated CD4+ T cells by negative selection

tag: hiv-1 infection status

value: Uninfected


title: ATAC_VAL_8h_r1

description:
Replicate 1
Diff_Peak_Down_VAL_AZ4573_8h_vs_VAL_DMSO.bed

tag: cell line

value: 8 hours


title: 2023Rep1Feature Barcoding


title: Panc1 Gem 24h Drop-seq

source_name: Panc1 treated with 2 µM Gemcitabine

value: Treated for 24 h


title: fastATAC_VAL_8h_r1

value: Fast-ATAC-seq (5,000 cells)


title: ATAC_VAL_3h_r1

value: 3 hours


title: ATAC_VAL_3h_r2


title: H3K4me1_Input_T00

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction


title: D31

value: major depressive disorder patients

value: Cubital vein peripheral whole blood


title: 2004Feature Barcoding


title: DS910Feature Barcoding

value: Suppressed


title: ATAC_VAL_0h_r2

description: Replicate 2

value: 0 hours


title: fastATAC_VAL_0h_r2

description: Replicate 2

value: VAL


title: H3K4me1_T24_rep2

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction

tag: chip antibody

value: anti-H3K4me1 antibody (Diagenode c15410037), at 2.5 microgram per 10e6 cells


title: ATAC_OCI_LY3_8h_r2

value: Standard ATAC-seq (50,000 cells)


title: ATAC_VAL_0h_r1

description: Replicate 1


title: H3K4me1_Input_T20

value: 20 Hours (T20)

value: ASCs on 20 hours after adipogenic induction


title: fastATAC_VAL_0h_r1

description: Replicate 1


title: H3K4me1_T20_rep2


title: ATAC_OCI_LY3_3h_r2


title: ATAC_OCI_LY3_8h_r1

value: 8 hours


title: DV910Feature Barcoding

value: Isolated unstimulated CD4+ T cells by negative selection

value: Viremic


title: H3K4me1_T20_rep1


title: H3K4me1_T24_rep1


title: ATAC_OCI_LY3_3h_r1

value: 3 hours


title: IS640Feature Barcoding


title: IV640Feature Barcoding


title: ATAC_OCI_LY3_0h_r2

description: Replicate 2


title: ATAC_OCI_LY3_0h_r1

description: Replicate 1


title: H3K4me1_T16_rep2

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction


title: 2023Rep2scRNA-seq

description:
M2filtered_contig_igblast_db-pass_parse-select.tab
M2matrix.tar

data_processing:
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

value: Uninfected


title: GW23.0_PV_BP

city: San Francisco

first: Bryan

middle: P

last: Marsh

state: CA

address: 35 Medical Center Way, RMB 912E, None

institute: University of California, San Francisco

data_processing:
Processing of raw sequencing to a counts matrix was performed using CellRanger v3.0.2 using default settings. This includes alignment to the GRCh38 genome using STAR (v2.6). Processing of counts matrix was performed in Seurat v3.1.3. Raw counts were normalized, scaled, and batch corretion and integration performed using Seurat. Additional details can be found in the manuscript (Marsh et al., 2022).
Assembly: GRCh38

source_name: Single Cell RNA-seq data from human placental cells

extract_protocol:
Cell isolation protocols described in Marsh  et al., 2022 - PV/BP isolation described in Fisher et al., 1989; Kliman and Feinberg, 1990; SC isolation described in Garrido-Gomez et al., 2017
10x Genomics Single Cell 3' v3 Protocol

tag: gestational age

value: 23 weeks and 0 days post conception

tag: placental region

value: Cells Isolated from the Placental Villi and Basal Plate


title: H3K4me1_T16_rep1

city: Oslo

tag: time point

tag: replicate


title: GW23.0_SC

value: Cells Isolated from the Smooth Chorion


title: GW17.6_SC

value: 17 weeks and 6 days post conception


title: GW17.6_PV_BP


title: 2023Rep1scRNA-seq

description:
M1filtered_contig_igblast_db-pass_parse-select.tab
M1matrix.tar


title: GW18.2_PV_BP

value: 18 weeks and 2 days post conception


title: H3K4me1_T12_rep2

value: 12 Hours (T12)

value: ASCs on 12 hours after adipogenic induction


title: GW24.0_PV_BP

value: 24 weeks and 0 days post conception


title: H3K4me1_T12_rep1

value: anti-H3K4me1 antibody (Diagenode c15410037), at 2.5 microgram per 10e6 cells


title: 2004scRNA-seq

description:
M3filtered_contig_igblast_db-pass_parse-select.tab
M3matrix.tar


title: DS910scRNA-seq

description:
DS910filtered_contig_igblast_db-pass_parse-select.tab
DS910matrix.tar

value: Suppressed


title: SF7761_GS_3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Base calling was performed using Casava (Illumina).
Reads were trimmed using Trimmomatic v0.36 (Bolger et al. Bioinformatics, 2014) with parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:25 SLIDINGWINDOW:4:15.
Single-end alignments and gene level counts were obtained using RSEM v1.3.1 (Li and Dewey. BMC Bioinformatics, 2011). STAR v2.5.2a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics, 2013).
The human reference sequence hg38/GRCh38 and annotations, including gene IDs, were obtained from GENCODE v. 29 (Frankish et al. Nucleic Acids Res. 2018).
Supplementary files: sample expression matrices (tab-delimited text with headers) with counts, FPKM, and TPM are provided for both genes and transcript isoforms. The first two columns contain gene/transcript IDs.
Genome_build: hg38
Supplementary_files_format_and_content: Quantification files for both genes and transcript isoforms are provided for each sample in tab-delimited text files containing headers.  See RSEM documentation for more detail on contents.

source_name: pediatric diffuse intrinsic pontine glioma (DIPG) cell line

growth_protocol: HSJD-DIPG-007 (referred to as DIPG-007, H3.3K27M), DIPG-XIII (H3.3K27M), SF188 (H3WT), normal human astrocytes (NHA; H3WT) were obtained from the Venneti laboratory after MTA from the respective collaborators and institutions. SF7761 (H3.3K27M) was purchased from Millipore Sigma (Cat.no. SCC126). The cells were cultured in a humidified incubator at 37°C and 5% CO2. DIPG007 and DIPG-XIII gliomaspheres were cultured in base media containing equal parts Neurobasal A and DMEM/F12 with added HEPES buffer (10 mM), MEM sodium pyruvate solution (1mM), MEM Non-Essential Amino Acids (1X), GlutaMAX-I Supplement (1X), Antibiotic-Antimycotic (1X), and supplemented with fresh B27 (without vitamin A),  heparin (2 μg/mL), human-EGF (20 ng/mL), human-bFGF (20 ng/mL), PDGF-AA (10 ng/mL), and PDGF-BB (10 ng/mL). SF7761 gliomaspheres were cultured in a base media containing Neurobasal A with added N2, B27, L-glutamine (2 mM), Pen/strep (1X), and supplemented with fresh heparin (2 μg/mL), human-EGF (20 ng/mL), human-bFGF (20 ng/mL), and BSA (45 ng/ml). Differentiated glioma cells were generated by dissociating DIPG gliomaspheres into single cells with Accutase and subsequently cultured and maintained in the respective base media supplemented with 10% FBS for 14 days to generate a monolayer adherent culture. SF188 and NHA cells were cultured in DMEM supplemented with FBS (10%), L-glutamine (2 mM), and Pen/strep (1X). All cell lines used were routinely tested for mycoplasma and were validated by STR profiling.

extract_protocol:
Differentiated glioma cells were generated by dissociating DIPG gliomaspheres into single cells with Accutase and subsequently cultured and maintained in the respective base media supplemented with 10% FBS for 14 days to generate a monolayer adherent culture. SF188 and NHA cells were cultured in DMEM supplemented with FBS (10%), L-glutamine (2 mM), and Pen/strep (1X).
Strand-specific, poly-A+ libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolab, E7760L), the Poly(A) mRNA Magnetic Isolation Module (New England Biolab, E7490L), and NEBNext Multiplex Oligos for Illumina Unique Dual (New England Biolab, E6440L).

tag: culture state

value: gliomaspheres


title: H3K4me1_T08_rep2

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction


title: SF7761_GS_2


title: DV910scRNA-seq

description:
DV910filtered_contig_igblast_db-pass_parse-select.tab
DV910matrix.tar

value: Isolated unstimulated CD4+ T cells by negative selection

value: Viremic


title: SF7761_GS_1


title: SF7761_DGC_1

value: differentiated glioma cells


title: SF7761_DGC_3


title: H3K4me1_T04_rep2

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: DIPG13_GS_3


title: IV640scRNA-seq

description:
IV640filtered_contig_igblast_db-pass_parse-select.tab
IV640matrix.tar


title: DIPG13_GS_1


title: INPUT_Dm2 [re-analysis]

description: re-analysis of GSM3394772

value: Day -2 (proliferative; "Pro")

value: Proliferating adipose stem cells (ASCs) in growth medium


title: H3K4me1_T00_rep2

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction


title: DIPG13_DGC_3


title: INPUT_D0 [re-analysis]

description: re-analysis of GSM3394771

value: 72 Hours (T72)

value: ASCs on 72 hours after adipogenic induction


title: DIPG13_DGC_2


title: DIPG13_DGC_1


title: INPUT_Ad-D3 [re-analysis]

description: re-analysis of GSM3394770

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction


title: DIPG007_GS_3


title: RNAseq_T72_Rep2


title: DIPG007_GS_2


title: RNAseq_T72_Rep1


title: INPUT_Ad-D1 [re-analysis]

description: re-analysis of GSM3394769


title: GW18.2_SC

value: 18 weeks and 2 days post conception

value: Cells Isolated from the Smooth Chorion


title: DIPG007_DGC_3


title: DIPG007_GS_1

value: gliomaspheres


title: GW24.0_SC

value: 24 weeks and 0 days post conception


title: D3_LMNB1_Rep3 [re-analysis]

description: re-analysis of GSM3394762

value: anti-lamin B1 antibody (Abcam ab16048), at 10 microgram per 10e7 cells


title: DIPG007_DGC_2


title: RNAseq_T24_Rep2


title: DIPG007_DGC_1


title: D3_LMNB1_Rep2 [re-analysis]

description: re-analysis of GSM3394758


title: H3K4me1_T08_rep1

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction

value: anti-H3K4me1 antibody (Diagenode c15410037), at 2.5 microgram per 10e6 cells


title: RNAseq_T24_Rep1


title: H3K4me1_Input_T72


title: SF7761_DGC_2

value: differentiated glioma cells


title: H3K4me3_H3K27ac_Input_T72


title: IS640scRNA-seq

description:
IS640filtered_contig_igblast_db-pass_parse-select.tab
IS640matrix.tar

value: Isolated unstimulated CD4+ T cells by negative selection

value: Suppressed


title: D1_LMNB1_Rep3 [re-analysis]

description: re-analysis of GSM3394761


title: RNAseq_T20_Rep2

value: 20 Hours (T20)

value: ASCs on 20 hours after adipogenic induction


title: H3K4me1_T04_rep1

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: H3K4me1_T72_rep1

description:
T72_H3K4me1_peaks.broadPeak
H72_H3K4me1.bw

value: 72 Hours (T72)

value: ASCs on 72 hours after adipogenic induction


title: H3K4me1_T72_rep2


title: DIPG13_GS_2


title: D1_LMNB1_Rep2 [re-analysis]

description: re-analysis of GSM3394757

value: 24 Hours (T24)

value: ASCs on 24 hours after adipogenic induction


title: H3K4me3_T72_rep1

value: anti-H3K4me3 antibody (Diagenode c15410003), at 2.5 microgram per 10e6 cells


title: RNAseq_T20_Rep1


title: H3K4me1_T00_rep1

value: 00 Hours (T00)

value: ASCs on the day of differentiation induction


title: RNAseq_T16_Rep2

value: 16 Hours (T16)

value: ASCs on 16 hours after adipogenic induction


title: Treat3-IP

city: Beijing

first: Dong

last: Han

address: No. 28, Fuxing Road, Haidian District

institute: 301 PLA hospital

data_processing:
Library strategy: MeRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For  MeRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
hg38

source_name: Human cardiomyocyte

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).

value: myocardial cell

tag: treatment

value: IP


title: Treat3-input


title: D0_LMNB1_Rep3 [re-analysis]

description: re-analysis of GSM3394760

value: anti-lamin B1 antibody (Abcam ab16048), at 10 microgram per 10e7 cells


title: D0_LMNB1_Rep2 [re-analysis]

description: re-analysis of GSM3394756


title: RNAseq_T16_Rep1


title: Treat2-input


title: Pro_LMNB1_Rep2 [re-analysis]

description: re-analysis of GSM3394759

value: Day -2 (proliferative; "Pro")

value: Proliferating adipose stem cells (ASCs) in growth medium


title: Treat1-IP


title: RNAseq_T12_Rep2

value: 12 Hours (T12)

value: ASCs on 12 hours after adipogenic induction


title: Treat1-input


title: Pro_LMNB1_Rep1 [re-analysis]

description: re-analysis of GSM3394755


title: RNAseq_T12_Rep1


title: NC3-IP


title: KOH3K27acIP-3

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
ChIP-seq reads were aligned to the GENCODE release 25 genome assembly or mouse GENCODE release 18 using Bowtie2 v2.3.5
Multimapping reads removed with samtools v1.9 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.21.4
peaks were called using  MACS2 version 2.2.7.1
IDR analysis was performed by IDR Filter v1.2
Genome_build: GENCODE release 25 and mouse GENCODE release 18
Supplementary_files_format_and_content: bed files were generated using MACS2 version 2.2.7.1

source_name: human K562 cells

growth_protocol: Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum. Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Briefly, 30X106 K562 cells were fixed with 1% formaldehyde, sonicated and immunoprecipitated with antibodies against H3K27ac, HA and BRG1 . Chromatin was pulled down using Dynabeads Protein G, washed twice with RIPA-LS, RIPA-HS, LiCL washing buffer, followed by one wash with 10mM TrisHCl pH8.0. Precipitated DNA was reverse cross link and eluted for ChIP or was tagmentated (ChIPmentation)on magnetic beads with 0.2ul of tagmentation enzyme (Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024) for 10 minutes at 37 degree while shaking. The beads with tagementated DNA were washed twice with RIPA-LS and TE buffers. The DNA was eluted and de-crosslinked in ChIP elution buffer (20 mM Tris, pH 7.5, 5 mM EDTA, pH 8.0, 50 mM NaCl, 1% SDS, and 50 μg/mL proteinase K) for 1 hour at 55 degree and incubated at degree  overnight.
ChIP-mentation Libraries were prepared using Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024. Eluted DNA was purified using SRI beads (1.8x) and PCR amplified with Nextera primers. Libraries were purified (1.8x) and size selected (0.65x/ 0.15x) with SRI beads. ChIP Libaries were processing followed manufacturer’s protocol (Takara Bio, R400675)

tag: genotype

value: hemogen KO


title: RNAseq_T08_Rep2

value: 08 Hours (T08)

value: ASCs on 08 hours after adipogenic induction


title: Treat2-IP


title: NC1-IP


title: NC1-input


title: KOH3K27acIP-2


title: NC2-input


title: RNAseq_T08_Rep1


title: RNAseq_T04_Rep2

value: 04 Hours (T04)

value: ASCs on 04 hours after adipogenic induction


title: KOH3K27acIP-1


title: KOinput-3


title: pooled m3hcfeaturebarcoding

description:
m3hcbarcodes.tsv.gz
m3hcfeatures.tsv.gz
m3hcmatrix.mtx.gz

value: antigen stimulated CD4+ T cells


title: pooled m2hcfeaturebarcoding

description:
m2hcbarcodes.tsv.gz
m2hcfeatures.tsv.gz
m2hcmatrix.mtx.gz


title: KOinput-2


title: RNAseq_T04_Rep1


title: pooled m2hmfeaturebarcoding

description:
m2hmbarcodes.tsv.gz
m2hmfeatures.tsv.gz
m2hmmatrix.mtx.gz


title: pooled m2cmfeaturebarcoding

description:
m2cmbarcodes.tsv.gz
m2cmfeatures.tsv.gz
m2cmmatrix.mtx.gz


title: RNAseq_T00_Rep2

value: 00 Hours (T00)


title: H3K27ac_T72_rep1

value: 72 Hours (T72)

value: ASCs on 72 hours after adipogenic induction

value: anti-H3K27ac antibody (Diagenode c15410174), at 2.5 microgram per 10e6 cells


title: pooled m1hmfeaturebarcoding

description:
m1hmbarcodes.tsv.gz
m1hmfeatures.tsv.gz
m1hmmatrix.mtx.gz


title: RNAseq_T00_Rep1

value: ASCs on the day of differentiation induction


title: KOinput-1


title: pooled m1hcafeaturebarcoding

description:
m1hcabarcodes.tsv.gz
m1hcafeatures.tsv.gz
m1hcamatrix.mtx.gz


title: pooled m1cmfeaturebarcoding

description:
m1cmbarcodes.tsv.gz
m1cmfeatures.tsv.gz
m1cmmatrix.mtx.gz


title: NC3-input

value: myocardial cell


title: pooled hdm2featurebarcoding

description:
hdm2barcodes.tsv.gz
hdm2features.tsv.gz
hdm2matrix.mtx.gz

value: Uninfected


title: pooled m3mscTCR

description:
m3m_all_contig.fasta
m3m_all_contig_annotations.csv

data_processing:
Library strategy: TCR-seq
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)


title: WTH3K27acIP-3

value: WT


title: pooled hdcmvfeaturebarcoding

description:
hdcmvbarcodes.tsv.gz
hdcmvfeatures.tsv.gz
hdcmvmatrix.mtx.gz


title: pooled hdm1featurebarcoding

description:
hdm1barcodes.tsv.gz
hdm1features.tsv.gz
hdm1matrix.mtx.gz


title: pooled m2hmscTCR

description:
m2hm_all_contig.fasta
m2hm_all_contig_annotations.csv


title: pooled m3hcscTCR

description:
m3hc_all_contig.fasta
m3hc_all_contig_annotations.csv


title: WTH3K27acIP-2


title: WTH3K27acIP-1


title: WTinput-3


title: pooled m2cmscTCR

description:
m2cm_all_contig.fasta
m2cm_all_contig_annotations.csv


title: NC2-IP

value: IP


title: pooled m3mfeaturebarcoding

description:
m3mbarcodes.tsv.gz
m3mfeatures.tsv.gz
m3mmatrix.mtx.gz


title: m6A_IP_uninfected

last: Chen

data_processing:
Library strategy: meRIP-seq
Illumina bcl2fastq software used for base-calling
reads algined to corresponding genomes (hg19 for human and mm9 for mouse) using TopHat (stranded), converted to sorted BAM using SAMTools, and further processed using exomePeak
gene count measurements were obtained using HTSeq-count
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: cervical carcinoma/epithelial cells

extract_protocol:
Total RNA were extraction follows TRI reagent protocol (Thermo-Fisher) and then treated with DNase I to remove DNA contamination. . For m6A MeRIP-seq, the m6A enrichment were performed using m6A antibody (m6A antibody cat#202203, synaptic systems) and m6A-enriched and fragmented RNA was purified using RNeasy Mini Kit as IP.
KAPA Stranded RNA-seq Kit (Illumina) was used for the library preparation of both m6A-IP RNA and input mRNAs. The quality of the completed libraries was performed with Agilent 2100 Bioanalyzer

value: Hela

value: Control/ununinfected

tag: rna harvest

value: Enrichment of m6A methylated mRNA with m6A antibody (Abcam, ab208577)


title: huh7 cells miR-383 transfected and DENV infected

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetric Expression Console using default analysis settings

label: Biotin

source_name: Huh7 cells transfected with miR-383 mimic andinfected with DENV

label_protocol: Biotinylated cRNA were prepared using the Affimetrix GeneChip™ WT PLUS Reagent Kit with Biotin Allonamide Triphosphate from 5.5 ug total RNA

growth_protocol: Human hepatoma (Huh7) cells  were grown at 37°C in DMEM (Gibco, Life Technologies) with 10% FBS (Wisent) and 10 mM non-essential amino acids.

extract_protocol: RNA isolation was performed using the Norgen total RNA isolation kit as per manufacturer’s protocol

treatment_protocol: One day prior to treatment, cells were seeded at 2x10^5 cells per well in a 6-well plate. The following day, cells were transfected with either con-miR or miR-383. For DENV infected conditions, cells were infected at an MOI of 0.1 24h post-transfection and lysed 48h post infection. For non-infected conditions, cells were lysed for RNA isolation 72h post-transfection.


title: pooled m1hcbfeaturebarcoding

description:
m1hcbbarcodes.tsv.gz
m1hcbfeatures.tsv.gz
m1hcbmatrix.mtx.gz


title: pooled m1hmscTCR

description:
m1hm_all_contig.fasta
m1hm_all_contig_annotations.csv


title: huh7 cells miR-383 transfected

source_name: Huh7 cells transfected with miR-383 mimic


title: m6A_IP_5h

value: 5hr after HSV-1 infection


title: huh7 cells con-miR transfected

source_name: Huh7 cells transfected with con-miR mimic


title: huh7 cells con-miR transfected and DENV infected

source_name: Huh7 cells transfected with con-miR mimic and infected with DENV


title: m6A_IP_8h

value: 8hr after HSV-1 infection


title: pooled hdm2scTCR

description:
hdm2_all_contig.fasta
hdm2_all_contig_annotations.csv


title: pooled hdcmvscTCR

description:
hdcmv_all_contig.fasta
hdcmv_all_contig_annotations.csv


title: WTinput-1


title: pooled m1hcbscTCR

description:
m1hcb_all_contig.fasta
m1hcb_all_contig_annotations.csv


title: pooled m3hcscRNAseq

description:
m3hcbarcodes.tsv.gz
m3hcfeatures.tsv.gz
m3hcmatrix.mtx.gz


title: K562 WT-3, RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...

growth_protocol: Primary CD34+ umbilical cord cells (Lonza, cat. 2C-101) were cultured as described (Wilber et al., 2010). HUDEP2 cells was cultured in SFEM medium and induced in DMEM medium as described (Vinjamur and Bauer, 2018). K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.


title: WTinput-2


title: pooled m1hcascTCR

description:
m1hca_all_contig.fasta
m1hca_all_contig_annotations.csv


title: K562 WT-2, RNA-seq


title: pooled m2hcscTCR

description:
m2hc_all_contig.fasta
m2hc_all_contig_annotations.csv


title: K562 hemogen KO-2, RNA-seq

value: hemogen KO


title: 3a1KO_Hippocampus_RNA_3

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine

data_processing:
STAR v2.5.4a was used to map to the genome. Gencode.mouse.v1.annotation.gtf was used for gene annotation.
2-pass strategy of STAR was used, see https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ for more details.
htseq/0.11.0 was used to calculate the raw read counts for each gene. htseq-count -m intersection-nonempty -i gene_id -s reverse -r pos -f bam
Genome_build: mm9

source_name: Hippocampus

extract_protocol:
The hippocampus were isolated, crushed and homogenized. Total RNA were purified with AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-Seq libraries were prepared with TruSeq® Stranded mRNA Library Prep (illumina).

tag: tissue

value: Hippocampus

tag: strain

tag: developmental stage

value: postnatal day 21


title: pooled m1hmscRNAseq

description:
m1hmbarcodes.tsv.gz
m1hmfeatures.tsv.gz
m1hmmatrix.mtx.gz

value: antigen stimulated CD4+ T cells


title: pooled m1cmscTCR

description:
m1cm_all_contig.fasta
m1cm_all_contig_annotations.csv


title: pooled m3mscRNAseq


title: pooled m1hcbscRNAseq


title: K562 hemogen KO-1, RNA-seq


title: Input_uninfected

city: San Antonio

first: Yidong

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health Science Center at San Antonio

value: Input RNA


title: Input_HSV_1_8h


title: K562 hemogen KO-3, RNA-seq