title: RNA-seq_MONO_2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

description:
Mononuclear cells isolated from peripheral blood
FPKM of all genes for  MONO and TAMs.xlsx

data_processing:
Reads from RNA-seq experiments were aligned to hg19 genome using STAR.
Duplicate reads were removed with SAMtools.
The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff and R packages.
Genome_build: hg19
Supplementary_files_format_and_content: The bw (BigWig) files were generated using deepTools.

source_name: MONO cells

extract_protocol:
Total RNA product was purified using RNeasy Mini Kit (QIAGEN, Germany) and run-on Agilent Bioanalyzer 4200 to assess RNA integrity.
The total RNA‐seq library preparation from total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions.

value: MONO cells

value: untreated


title: Patient1391_HLAG_EVT

status: Public on Aug 10 2021

type: genomic

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

description: Genomic DNA was extracted from placental tissue or MSCs and hybridized to the Illumina InfiniumOmni2-5-8v1-4 BeadChip

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing: Samples were called in GenomeStudio (Illumina) with an average overall call rate of 99.4%. The CTB sample from one patient (1391) was removed from the analysis due to a low call rate (91.3%). CNVs were identified using the cnvPartition Plug-in (v. 3.2.0) in GenomeStudio. The cnvPartition confidence threshold was set at 100, with a minimum number of SNPs per CNV region of 10. The R (v. 3.6.1) package, allele-specific copy number analysis of tumors (ASCAT) (v. 2.5.2) (Van Loo, 2010 PMC2947907), was used to estimate the ploidy of EVT samples. LogR ratios and BAF values were exported from GenomeStudio and no GC wave correction was performed. EVT samples were considered “tumor” samples and matched UC-MSCs were used as “reference” samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: first trimester placental tissue

label_protocol: Standard Illumina Protocol

growth_protocol: First and term placentae tissues were collected under a UCSD Human Research Protections Program Committee Institutional Review Board-approved protocol; all patients provided informed consent for collection and use of these tissues. Term placentae was obtained immediately after C-section and placed on ice. For first trimester placentae, “normal” refers to elective termination of pregnancy in the absence of structural fetal abnormalities; for third trimester placentae (term), “normal” is defined by a non-hypertensive, non-diabetic singleton pregnancy, where the placenta is normally grown and shows no gross or histological abnormalities. Human umbilical cord (UC) was collected aseptically under a protocol approved by the Human Research Protections Program Committee of the UCSD Institutional Review Board (IRB number: 181917X). All patients provided informed consent for collection and use of these tissues, and all experiments were performed within guidelines and regulations set forth by the IRB. Umbilical cord mesenchymal stem cells (UC-MSCs) were derived from minced umbilical cord tissue per a published protocol (PMID: 19657615, 25058409) from umbilical cord (UC) samples that were collected and processed within 24 hours of delivery.

extract_protocol: DNA was isolated from placental cell pellets from two first trimester and three term placentae (Qiagen DNeasy Blood and Tissue kit) and quantified (Qubit dsDNA BR Assay Kits, Thermo Fisher Scientific) according to the manufacturer’s protocol. DNA from matched UC-MSCs from the three term placental patients were isolated in the same manner.

treatment_protocol: UC’s were minced and washed to remove blood and then cultured in basal medium (aMEM with nucleotide (ThermoFisher), containing 10% MSC-qualified FBS (OmegaScientific)). Cultures were maintained in a humidified atmosphere with 5% CO2 at 37°C. Approximately three weeks after plating, adherent fibroblast-like cells were detached using TrypLE Express for 5 minutes at 37oC (ThermoFisher) and filtered to remove any tissue fragments. The collected cells were then reseeded and maintained in growth medium containing b-FGF.   After two weeks of growth with medium replacement every three days, the cells were checked for purity by flow cytometry analysis (BD FACSCanto 2 HTS). Cells were assessed for the expression of CD73 (FITC Mouse Anti-Human CD73 – BD #561254) and the absence of CD31 (APC-Cy™7 Mouse Anti-Human CD31 BD #563653) and CD45 (APC Mouse Anti-Human CD45 – BD #560973). UC-MSCs samples displayed CD73 expression in over 90% of cells and 0% expression of CD31 and CD45. Sex of first trimester cell samples was determined based on PCR for SRY. Isolation of cytotrophoblast (CTB) and extravillous trophoblast (EVT) from term placentae (37- to 41-weeks GA) was performed as previously described in (PMID: 24004950). Tissue from the basal plate (for EVT) and chorionic portion (for CTB) was dissected and minced, rinsed in 1X PBS (Corning), and digested for 20 minutes in 1X Ca/Mg-free HBSS (Gibco), 1X trypsin (Gibco), collagenase, and DNase (Roche) three times, discarding the supernatant after each digestion. A Percoll gradient (Sigma-Aldrich) centrifugation separation was then performed. Cells were then subjected to positive selection using magnetic activated cell sorting (MACS) (Miltenyi Biotec) and a PE-conjugated antibody against HLA-G (EXBIO MEM-G/9). The bound fraction was collected, tested for purity using flow cytometry. EVT preparations that contained greater than 90% HLA-G+ cells were considered as adequate and used in downstream experiments. The unbound fraction was collected and CTB were selected using APC-conjugated antibody against EGFR (Biolegend #352906;) and tested for purity using flow cytometry. CTB preparations yielding greater than 90% EGFR positivity were considered adequate and used in downstream experiments. Isolation of primary first trimester (9- to 14-week gestational age) trophoblast cells from placenta samples was performed as previously described in (PMID: 28167044, 29361559).  Briefly, chorionic villi were minced, washed in Hanks’ balanced salt solution (Gibco) and digested three times with DNase I (Roche) and trypsin (Gibco). The cells were then pelleted and separated on a Percoll gradient (Sigma-Aldrich) and subjected to sequential MACS selection similar to the term placental samples.

tag: gender

value: Female

tag: cell type

value: EVT

tag: ga (gestational age wks)


title: Normoxia_rep5

type: SRA

city: Schlieren

first: Lynn

middle: Jenny Alix

last: Ebner

state: Zürich

address: Wagistrasse 14

department: Department of Ophthalmology

country: Switzerland

institute: Universität Zürich

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRC38p5 whole genome using STAR
Genome_build: GRC38p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas were isolated through a slit in the cornea and snap-frozen in liquid nitrogen. RNA was isolated using an RNA isolation kit (Nucleo Spin RNA, Macherey-Nagel GmbH & Co.KG, Düren, Germany) with an additional, on-column DNase I treatment according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For all experiments performed in Zurich (ZH), mice were placed in their homecage in isobaric hypoxia chambers and exposed to hypoxia for 6 h, 48 h, or 11 weeks. Briefly, oxygen concentration was decreased gradually by 2% every 10 min by altering the oxygen:nitrogen ratio until either 14% or 7% O2 was reached. For hypobaric experiments performed at high altitude (JFJ), mice were exposed to the environmental air pressure of approximately 64.65 kPa (slightly fluctuating depending on weather and time of the year), which decreases the ambient partial pressure of oxygen from 21.2 kPa (sea level) to 13.7 kPa

tag: strain

tag: tissue

value: Retina

tag: condition

value: normoxia


title: Human monocytes RNA-seq VACV replicate 3

city: Beijing

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

country: China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: VACV treatment

data_processing:
The original data was filtered through the quality control software fastp, and the Hista2 software was used to compare with the reference gene sequence. The reference genome is Hg38. The gene information is downloaded from the NCBI database.
The featureCounts software is used to calculate the gene expression between samples. Perform gene differential expression analysis on the two sets of samples through the R package DESeq2 software.
Genome_build: Hg38
Supplementary_files_format_and_content: Txt files for the DESeq2 results of RNA-seq

source_name: Human monocytes(THP-1)

extract_protocol:
Total RNAs were isolated from embryos at the indicated stages using TRIzol reagent (TIAN GEN).
To RNA-seq,  Illumina Truseq libraries were constructed according to the manufacturer’s instructions and sequenced using NovaSeq platform. with paired end read length of 150 bp. RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

value: monocytes (THP-1)

tag: age


title: Patient1386_EGFR_CTB

value: CTB


title: Normoxia_rep3


title: Human monocytes RNA-seq replicate  mock 3

description: MOCK


title: Normoxia_rep1


title: Patient2754_HLAG_EVT

source_name: term placental tissue


title: Normoxia_rep4


title: Patient2771_HLAG_EVT

value: Male


title: 07-06h-ZH_rep3

value: hypoxia

tag: time point

tag: location

value: Zurich (400masl)


title: Normoxia_rep2


title: Normoxia_rep6


title: RNA-seq_TAM_2

description:
TAMs isolated from human PDAC tissues
FPKM of all genes for  MONO and TAMs.xlsx

source_name: TAMs cells

value: TAMs cells

tag: treatment


title: RNA-seq_TAM_1


title: Patient1386_HLAG_EVT


title: Human monocytes RNA-seq replicate  mock 1

description: MOCK


title: Human monocytes RNA-seq replicate  mock 2

description: MOCK


title: RNA-seq_MONO_1


title: Human monocytes RNA-seq VACV replicate 1

description: VACV treatment


title: B6 [B6_3]

status: Public on Aug 09 2021

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were demultiplexed the reads into the different samples
Reads were aligned to the hg19 genome built using Tophat (v2.0.10)
Read counting to Refseq genes was done with HTseq-count (version 0.6.1p1)
DESeq2 (1.6.3) was used for the normalization
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes the raw counts and DESeq2 normalized counts

growth_protocol: PC9 cell line was grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, pyruvate and glutamine .

extract_protocol:
2x10^6 cells from each clone were seeded on a 10cm plate and left to settle overnight. Total RNA from different samples was extracted using the Direct-Zol RNA mini-prep kit (Zymo-research) according to the manufacturer’s protocol. The RNA integrity of all samples was assessed by Bioanalyzer to ensure an RNA integrity number (RIN) score of at least 9 before proceeding to library preparation. Next, 1μg of RNA from each sample was taken for preparation of an mRNA TrueSeq library
Inhouse poly A based RNA seq

tag: % persisters relative to pc9 whole population


title: pupa0h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample2

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

library_source: genomic

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Genome_build: dm6 (dmel_r6.16_FB2017_03)
81 bigwigs are attached based on samples belonging to 10X_ADULT (adult brain) and to 10X_PUPA_72H
10X_ADULT and 10X_PUPA_72H samples were subset based on cell type and merged to acquire cell type specific bam files
bam files were then deduplicated, black listed regions removed and RPGC normalised to acquire bigwig files

organism: Drosophila melanogaster

source_name: Pupa Brain

extract_protocol:
D. melanogaster adult brains were dissected and transferred to a tube containing 100 µl ice cold DPBS solution. After centrifugation at 800 g for 5 min, the supernatant was replaced by 500 µl nuclei lysis buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, and 1% BSA, in Nuclease-free water. The following procedure was followed to extract the nuclei from the brain tissue: incubation in nuclei lysis buffer on ice for 5 min, transfer to a dounce tissue grinder tube (Merck), 25 strokes with pestle A, incubation on ice for 10 min, 25 strokes with pestle B. The lysis was stopped by adding 1 ml of wash buffer composed of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20 and 1% BSA, in Nuclease-free water. Nuclei were pelleted by centrifugation at 800 g for 5 min at 4°C and resuspended in 1x Nuclei Buffer (10x Genomics). Nuclei suspensions were passed through a 40 µM Flowmi filter (VWR Bel-Art SP Scienceware). Nuclei concentration was assessed by the LUNA-FL Dual Fluorescence Cell Counter.
10x Genomics CHROMIUM Single Cell ATAC Library & Gel Bead Kit v1

value: Brain

tag: developmental stage

value: Pupa

value: 0 hours

tag: genotype


title: B14 [B14_3]


title: pupa0h_brain_DGRP_mix_DGRP-551_Hyb-409-502-639_sample1


title: A10 [A10_2]


title: B14 [B14_2]


title: B6 [B6_2]


title: A10 [A10_3]


title: A7 [A7_2]


title: B6 [B6_1]


title: A7 [A7_3]


title: A7 [A7_1]


title: Cl.3 [Cl_3_2]


title: B24 [B24_3]


title: B24 [B24_2]


title: B24 [B24_1]


title: Cl.4 [Cl_4_3]


title: Cl.3 [Cl_3_1]


title: Cl.4 [Cl_4_2]


title: B14 [B14_1]


title: A10 [A10_1]


title: B12 [B12_1]


title: PC9 Whole Population [WP_1]

source_name: PC9 Whole Population


title: 6 week release [W6_Rel]

source_name: 6 week release

extract_protocol:
Total RNA from different samples was extracted using the Direct-Zol RNA mini-prep kit (Zymo-research) according to the manufacturer’s protocol. The RNA integrity of all samples was assessed by Bioanalyzer to ensure an RNA integrity number (RIN) score of at least 9 before proceeding to library preparation. Next, 1μg of RNA from each sample was taken for preparation of an mRNA TrueSeq library
Inhouse poly A based RNA seq

value: 6 weeks release from 9 days with gefitinib


title: PC9 naïve cells (never treated with drug) [WP]


title: PC9 Whole Population [WP_3]


title: Cl.4 PC9 derived clone [Clone_4]

source_name: Cl.4 PC9 derived clone


title: PC9 Whole Population [WP_2]


title: 2 week release [W2_Rel]

source_name: 2 week release

value: 2 weeks release from 9 days with gefitinib


title: 5 week release [W5_Rel]

source_name: 5 week release

value: 5 weeks release from 9 days with gefitinib


title: PC9 cells treated for 9 days with gefitinib and then released from drug for 3 additional days [Sample_46]

value: 3 days release from 9 days with gefitinib


title: Cl.3 [Cl_3_3]

value: untreated


title: 1.5 week release [W1_5_Rel]

source_name: 1.5 week release

value: 15 weeks release from 9 days with gefitinib


title: 13 week release [W13_Rel]

source_name: 13 week release

value: 13 weeks release from 9 days with gefitinib


title: 13 weeks naïve [W13_Na_ve]

source_name: 13 weeks naïve

value: Cells were grown without drug for 13 weeks


title: 2 weeks naïve [W2_Na_ve]

source_name: 2 weeks naïve

value: Cells were grown without drug for 2 weeks


title: Cl.4 [Cl_4_1]


title: PC9 cells treated for 9 days with gefitinib [Sample_45]

value: treated with gefitinib 9 days


title: 14 week release [W14_Rel]

source_name: 14 week release

value: 14 weeks release from 9 days with gefitinib


title: PC9 cells treated for 9 days with gefitinib and then released from drug for 3 additional days [Sample_44]


title: PC9 naïve cells [Sample_41]

source_name: PC9 naïve cells


title: B12 [B12_2]


title: PC9 cells treated for 9 days with gefitinib [Sample_39]


title: B12 [B12_3]


title: 11 treated total RNA replicate 4

city: Frederick

first: Curran

last: Rhodes

state: MD

address: 1050 Boyles St.

department: NCI

institute: NIH

description:
PN-4
Ligand, without PreQ1 aptamer spiked in

data_processing:
Reads were mapped to the longest isoform from RefSeq, using Bowtie v2 and the "--very-sensitive-local" preset
Genome_build: hg38

molecule: polyA RNA

source_name: MCF-7 human breast cancer cells

extract_protocol:
Total RNA was isolated from MCF-7 cells using the RNeasy mini kit (Qiagen) with on-column DNAse digestion
The sequencing libraries were prepared with the QiaSeq Stranded Total RNA Library Kit (Qiagen) by following the manufacturer's protocol

treatment_protocol: Isolated total RNA (5 ug, per sample) was added to the compounds and incubated for 30 mins.  Samples were UV-irradiated for 15 min at 365nm and click chemistry was used to install a biotin handle.  Modified RNAs were pulled down with SA-magnetic beads and sequencing libraries were prepared from the biotin-enriched RNA.

tag: cell line

value: MCF-7 human breast cancer cells

tag: compound treatment

value: Compound 11

tag: aptamer spike-in

value: NO


title: PC9 cells treated for 24h with gefitinib [Sample_42]

value: treated with gefitinib 24hr


title: PC9 cells treated for 24h with gefitinib [Sample_38]


title: PC9 cells treated for 9 days with gefitinib [Sample_40]


title: 11 treated total RNA replicate 3

description:
PN-3
Ligand, without PreQ1 aptamer spiked in


title: PC9 cells treated for 24h with gefitinib [Sample_36]


title: PC9 naïve cells [Sample_37]


title: 17 treated total RNA replicate 4

description:
NCN-4
Negative control probe, without PreQ1 aptamer spiked in

value: Compound 17


title: 11 treated total RNA replicate 1

description:
PN-1
Ligand, without PreQ1 aptamer spiked in


title: 11 treated total RNA replicate 2

description:
PN-2
Ligand, without PreQ1 aptamer spiked in


title: 11 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 1

description:
PY-1
Ligand, with PreQ1 aptamer spiked in

value: YES


title: PC9 naïve cells [Sample_35]


title: 11 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 3

description:
PY-3
Ligand, with PreQ1 aptamer spiked in


title: PC9 cells treated for 9 days with gefitinib and then released from drug for 3 additional days [Sample_43]


title: 11 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 4

description:
PY-4
Ligand, with PreQ1 aptamer spiked in


title: 11 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 2

description:
PY-2
Ligand, with PreQ1 aptamer spiked in


title: 17 treated total RNA replicate 1

description:
NCN-1
Negative control probe, without PreQ1 aptamer spiked in


title: 17 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 1

description:
NCY-1
Negative control probe, with PreQ1 aptamer spiked in


title: 17 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 2

description:
NCY-2
Negative control probe, with PreQ1 aptamer spiked in


title: hgsc_58

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

country: South Korea

institute: Cha University

data_processing:
All mRNA sequencing processing steps were in agreement with the guidelines proposed for TCGA mRNA-seq Pipeline for UNC data (https://webshare.bioinf.unc.edu/public/mRNAseq_TCGA/UNC_mRNAseq_summary.pdf) using Mapsplice-v2.1.8 and RSEM-1.1.13.
Genome_build: hg19
Supplementary_files_format_and_content: hgsc_raw_count.tsv file was generated by RSEM-1.1.13. Scores represent raw read counts.
Supplementary_files_format_and_content: hgsc_tpm.tsv file was generated by RSRSEM-1.1.13. Scores represent Transcripts Per Million (TPM).

source_name: high grade serous ovarian carcinoma

growth_protocol: The patients were divided into the following three groups based on their response to the first cycle of conventional adjuvant chemotherapy: no recurrence group, patients with no recurrence at ≥2 years from the end of first-line platinum-based chemotherapy; platinum-sensitive group, patients exhibiting recurrence 6 months after completing chemotherapy; platinum-resistance group, patients exhibiting recurrence within 6 months from ending first-line chemotherapy.

extract_protocol:
RNA was extracted from individual fresh snap-frozen tissue samples using TRIzol (Invitrogen) according to the manufacturer’s protocols. mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo attached magnetic beads.
RNA sequencing libraries were prepared using Illumina Truseq stranded mRNA Prep kit according to the manufacturer’s instructions. Cleaved RNA fragments primed with random hexamers were reverse transcribed into first strand cDNA. These cDNA fragments then had a single 'A' base added and were subsequently ligated to the adapter. The products were purified and enriched with polymerase chain reaction to create the strand specific cDNA library.

value: high grade serous ovarian carcinoma

tag: Stage

value: III

value: Platinum resistance

tag: survival

value: recurrence:Not available

value: Not available

tag: live/dead

value: live


title: hgsc_61

value: IV

value: dead


title: 17 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 3

description:
NCY-3
Negative control probe, with PreQ1 aptamer spiked in


title: hgsc_56


title: hgsc_60


title: hgsc_51


title: hgsc_54


title: 17 treated total RNA replicate 3

description:
NCN-3
Negative control probe, without PreQ1 aptamer spiked in


title: hgsc_44


title: hgsc_47

value: Platinum sensitive


title: hgsc_55


title: hgsc_48


title: hgsc_49


title: hgsc_33


title: hgsc_35


title: hgsc_53


title: 17 treated total RNA with BS-PreQ1 aptamer spiked-in replicate 4

description:
NCY-4
Negative control probe, with PreQ1 aptamer spiked in


title: hgsc_40


title: hgsc_42


title: hgsc_29


title: hgsc_28


title: hgsc_39


title: hgsc_32


title: hgsc_25


title: hgsc_24


title: hgsc_36


title: hgsc_43


title: hgsc_31


title: hgsc_22


title: hgsc_23

value: I


title: hgsc_30


title: hgsc_16


title: hgsc_20


title: hgsc_46


title: hgsc_41


title: hgsc_18


title: hgsc_17

value: No recurrence


title: hgsc_11


title: hgsc_13


title: hgsc_03


title: hgsc_08


title: hgsc_05


title: hgsc_12

value: II


title: hgsc_10


title: hgsc_21


title: hgsc_14


title: hgsc_38


title: hgsc_26


title: hgsc_15


title: Input Orc1 Flag#1

city: Boston

first: Xiaoyi

address: 240 Brookline Ave

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to the yeast genome assembly h90 using Bowtie-1.2.3 with default parameters
Peaks were called using MACS2-2.1.2 with the following parameters: -m 3 200 --bw 150  -g 1.38e7
Final peak set for each protein were defined by taking the overlap of two replicates using bedtools intersect with the following parameters:  -f 0.4 -r
Genome_build: h90
Supplementary_files_format_and_content: peak text files

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Cells were grown in rich media (YES) at 32C to OD1-2

extract_protocol:
Lysates were generated by bead beating followed by sonication. Lysate were incubated with beads with antibody at 4C for 3 hours.
Library for illumine sequencing was performed as previously described (ref) by following standard manufacture protocols, starting with 1-10ng immunoprecipitated DNA. Each library was generated by ligating with unique custom made adaptors. Libraries were pooled together and sequenced with Illumina HiSeq2500

treatment_protocol: Cells were incubated in 18C for two hours before fixation in formaldehyde at 18C for 30min

tag: strain number

value: SPM1047 h90 ade6-M210 leu1-32 ura4-D18, orc1::5xFLAG-orc1-kan

tag: antibody

value: Anti-Flag M2 (Sigma)


title: Input Deb1 Flag#2

value: h90 ade6-M210 leu1-32 ura4-D18, deb1-3xFLAG-hph


title: Input Orc1 Flag#2


title: hgsc_09

tag: tissue


title: WT Orc1 Flag#1


title: WT Orc1 Flag#2


title: hgsc_06


title: hgsc_04


title: Input Deb1 Flag#1


title: hgsc_02


title: WT Pcr1 Flag#2

value: h90 ade6-M210 leu1-32 ura4-D18, CenH{delta}::9xtetO-ura4 ,pcr1-3xFLAG-hph


title: WT Pcr1 Flag#1


title: WT Deb1 Flag#2


title: WT Deb1 Flag#1


title: WT Atf1 s1∆s2∆#2

value: h90 ade6-M210 leu1-32 ura4-D18, CenH{delta}::9xtetO-ura4 s1{delta}s2{delta},atf1-3xFLAG-hph


title: WT Atf1 s1∆s2∆#1

value: h90 ade6-M210 leu1-32 ura4-D18, CenH{delta}::9xtetO-ura4 s1{delta}s2{delta} ,atf1-3xFLAG-hph


title: WT Atf1 Flag#2

value: h90 ade6-M210 leu1-32 ura4-D18, CenH{delta}::9xtetO-ura4 ,atf1-3xFLAG-hph


title: WT Atf1 Flag#1


title: hgsc_01

value: high grade serous ovarian carcinoma

value: III


title: Non tag FLAG


title: m6A-IP_PCIF1 KO_HIV_rep1

city: La jolla

first: Qiong

state: California

address: 9500 Gilman Dr.

department: Pediatrics

description: Group 4_KO_HIV_pri.csv

data_processing:
Fastqc was used to perform quality control on sequencing data.
cutadapt was applied to remove adapters and trim reads.
The pre-processed reads were aligned to human genome (built on Release 31 (GRCh38.p12) gencode) by STAR
MACS2(q value: 0.05, call-summit mode) was used based on its paired m6A-RIP/input data.
To generate the peak distribution across chromosome region, including intron, CDS, intergenic region) and across gene region (3’UTR, 5’UTR and CDS) RSeQC and Guitar Plot were applied. The gene annotation used here is from GENCODE. For further m6Am peak analysis, we extracted common peaks whose summit is in the 5’UTR region.
Genome_build: GRCh38.p12

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI containing 10% fetal bovine serum (FBS) and 50 µM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted using TRIzol. About 200 μg RNA were then used to isolate poly(A) RNA using two rounds of oligo25 Dynabeads capture.
For one sample, 10 μg poly(A) RNA was de-capped with 10U Cap-Clip enzyme and was used for m6A-MeRIP experiment. Briefly, RNA was fragmented and incubated with 5 μg of anti-m6A antibody (abcam, ab151230) at 4 °C for 2 h. 100 μl protein G magnetic beads were added to pull down the m6A immunoprecipitation complex. After wash for three times, the bound RNA was eluted in 100 μl elution buffer and purified using RNA clean and concentrator-5 kit (Zymo Research). Final libraries amplified and were subjected to paired-end sequencing in the HT sequencing IGM Genomics core, UCSD.
MeRIP-seq

treatment_protocol: Ten million control or PCIF1 KO Jurkat cells were mock treated or infected with HIV LAI strain at an MOI of 4 for 3 days.

tag: chip antibody

value: anti-m6A antibody (abcam, ab151230)

value: T cell line


title: m6A-IP_PCIF1 KO_HIV_rep3

description: Group 4_KO_HIV_pri.csv


title: m6A-IP_PCIF1 KO_HIV_rep2

description: Group 4_KO_HIV_pri.csv


title: m6A-IP_PCIF1 KO_mock_rep2

description: Group 3_KO_mock_pri.csv


title: m6A-IP_PCIF1 KO_mock_rep3

description: Group 3_KO_mock_pri.csv


title: mAECs Yap/Taz knockout 3

type: RNA

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from tracheal epithelial cells treated with tamoxifen (Yap/Taz knockout).

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

source_name: tracheal epithelial cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Primary mAECs were grown to confluence on collagen coated transwell filters under submerged conditions.

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 3um 4-hydroxytamoxifen for 5 days to drive Cre recombinase activity and knockout.

value: tracheal epithelial cells

value: Yap/Taz knockout


title: m6A-IP_PCIF1 KO_mock_rep1

description: Group 3_KO_mock_pri.csv


title: mAECs Yap/Taz wild-type 1

description: Gene expression data from untreated tracheal epithelial cells (wild-type control).

value: Yap/Taz wild-type


title: mAECs Yap/Taz wild-type 3


title: mAECs Yap/Taz knockout 2


title: mAECs Yap/Taz knockout 1


title: HSCs Treated LPS rep6

city: Heidelberg

first: Yasmin

middle: Essam

last: Demerdash

state: Germany

address: Im Neunheimer Feld, 280

department: Inflammatory Stress in Stem Cells

country: Germany

institute: DKFZ

hyb_protocol: For expression analysis the samples were hybridised to the Illumina MouseWG-6 v2.0 Expression BeadChip® following the standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After normalisation the expression data was analysed using R. As the MicroArray includes several probes for some genes the data was _rst aggregated. Subsequently the means were calculated for all replicates of one treatment. These means were then used to calculate the fold changes between different treatments.

source_name: HSCs Treated LPS

label_protocol: Samples were amplified using the Ovation PicoSLWTA system and labeled with the BiotinILModule from NuGEN.

extract_protocol: RNA isolation was performed using the Arcturus PicoPure™ RNA Isolation Kit or the RNeasy Micro Kit (Qiagen). Cells were collected in 50 μl Extraction Buffer and lysed for 30 min at 42°C. Protocol was performed according to manufacturer’s instructions, including DNA digestion by RNase-free DNase (Qiagen). Quality control of the RNA was performed using a Agilent Bioanalyzer 2100.

treatment_protocol: Mice were treated with either PBS, IFNa or LPS for 18 hours

tag: strain

value: wildtype

tag: age

value: 8-10 week old mice

value: Treated LPS

value: Bone Marrow


title: HSCs Treated LPS rep1


title: mAECs Yap/Taz wild-type 2


title: HSCs Treated IFNa rep5

source_name: HSCs Treated IFNa

value: Treated IFNa


title: HSCs Treated IFNa rep4


title: m6A-IP_control_HIV_rep3

description: Group 2_HIV_pri.csv


title: HSCs Treated IFNa rep6


title: HSCs Treated LPS rep3


title: HSCs Treated IFNa rep1


title: HSCs Control PBStreated rep1

source_name: HSCs Control PBStreated

value: Control PBStreated


title: HSCs Treated LPS rep2


title: HSCs Treated IFNa rep2


title: HSCs Control PBStreated rep6


title: HSCs Treated IFNa rep3


title: BF5_CD14_RNASeq

city: Ithaca

first: Charles

middle: Grahe

last: Danko

state: NY

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
Data was processed using the Salmon pipeline (version 0.14.1), [PMID: 28263959].
Genome_build: rhemac10 (samples 1-5) papanu4 (samples 6-9)
Supplementary_files_format_and_content: The quant.sf file provides TPM for each NCBI transcript.

organism: Papio anubis

source_name: Primary CD14+ monocytes from PBMCs

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Female

tag: cell type


title: HSCs Treated LPS rep5

tag: treatment


title: HSCs Control PBStreated rep3


title: BM5_CD14_RNASeq


title: HSCs Control PBStreated rep5


title: HSCs Control PBStreated rep2


title: m6A-IP_control_HIV_rep1

description: Group 2_HIV_pri.csv


title: HSCs Treated LPS rep4


title: BF5_CD4_RNASeq

source_name: Primary CD4+ T-cells from PBMCs


title: HSCs Control PBStreated rep4


title: m6A-IP_control_mock_rep2

description: Group 1_control_pri.csv


title: m6A-IP_control_HIV_rep2

description: Group 2_HIV_pri.csv


title: BM5_CD4_RNASeq

value: Male


title: cells sampling at week 12_1 [Hashtag]

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

description:
w12_1_rawdata
w12_1_anno

data_processing:
The raw data were aligned to the hg19 reference genome using cellranger count (Version 3.0), and the hashed cells were demultiplexed using HTODemux function in Seurat 3, the cells aligned to doublet and negative group were removed from further analysis.
The Read1 was the technical for stroing UMI and barcode information, and 1-16nt indicates barocde and 17-28 refer to the UMI information.
Supplementary_files_format_and_content: comma-delimited csv files include UMI values and cell annotation for each cell

source_name: fetal hematopoietic, lymphoid and non-lymphoid tissues

extract_protocol: Single-cell RNA-seq library was prepared and performed on the Chromium platform(10X Genomics), using the single cell expression 3’ profiling chemistry combined with cell hashing. Cell-hashing antibody (HTO)-labeled cells from 2~3 tissues were pooled together and washed with RPMI-1640 immediately before loading on the 10X controller.Then library was constructed following the manufacturer’s protocol, with some additional steps for the amplification of HTO barcodes.

tag: time point

value: Week 12


title: cells sampling at week 10_1 [Hashtag]

description:
w10_1_rawdata
w10_1_anno

value: Week 10


title: L179483

city: beijing

first: lei

middle: lei

last: liang

address: panjiayuan

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

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60° C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65° C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37° C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: non-tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: no

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: no

tag: disease state

value: intrahepatic cholangiocarcinoma

value: liver

tag: tissue type

value: non-tumor

tag: gender

value: male


title: L178643


title: L182855


title: Input_PCIF1 KO_HIV_rep3

description: Group 4_KO_HIV_pri.csv

tag: cell line

value: T cell line


title: L180389


title: L177676


title: L181549


title: T182855

source_name: ICC

value: ICC


title: cells sampling at week 12_2 [Hashtag]

description:
w12_2_rawdata
w12_2_anno


title: m6A-IP_control_mock_rep1

description: Group 1_control_pri.csv

value: anti-m6A antibody (abcam, ab151230)


title: L179223


title: T178643


title: m6A-IP_control_mock_rep3

description: Group 1_control_pri.csv


title: cells sampling at week 10_2 [Hashtag]

description:
w10_2_rawdata
w10_2_anno


title: cells sampling at week 8_2 [Hashtag]

description:
w8_2_rawdata
w8_2_anno

value: Week 8


title: ComQ61R_3

city: Durham

first: Ozgun

last: Erdogan

state: NC

address: 308 Research Dr.

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
RNA-seq data was processed using the TrimGalore toolkit, which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20 nucleotides or longer after trimming were kept for further analysis.  Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.  Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Gene set enrichment analysis was performed to identify gene ontology terms and pathways associated with altered gene expression for each of the comparisons performed.
Supplementary_files_format_and_content: matrix table includes raw gene counts for every gene and every sample and their normalized expression with respect to the WT Kras allele.
Supplementary_files_format_and_content: Matrix table includes GSEA Hallmarks with respect to the WT Kras allele

source_name: Lung

extract_protocol:
All steps of tissue extraction, lysis, and RNA extraction were performed in a fume hood with tools sprayed with RNAZap. The lungs were harvested, stored in RNALater overnight, then stored at -80C for long-term storage. RNA extraction was performed with RNEasy Kit using QIAShredder columns for successful lysis and RNase-Free DNAse Set for removal of genomic DNA. Extracted total RNA quality and concentration was assessed on Fragment Analyzer (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific), respectively.  Samples with RIN less than 7 were not sequenced.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit (Roche).  In brief, mRNA transcripts were captured from 500 ng of total RNA using magnetic oligo-dT bead.  mRNA was then fragmented using heat and magnesium, and reverse transcribed using random priming.  During second strand synthesis, the cDNA:RNA hybrid was converted into to double-stranded cDNA (dscDNA) and dUTP was incorporated into the second cDNA strand, effectively marking this strand.  Illumina sequencing adapters were ligated to the dscDNA fragments and amplified to produce the final RNA-seq library.  The strand marked with dUTP was not amplified, allowing strand-specificity sequencing.  Libraries were indexed using a dual indexing approach allowing for all the libraries to be pooled and sequenced on the same sequencing run.  Before pooling and sequencing, fragment length distribution for each library was first assessed on a Fragment Analyzer (Agilent Technologies).  Libraries were also quantified using Qubit.  Molarity of each library was calculated based on qubit concentration and average library size.  All libraries were then pooled in equimolar ratio and sequenced.  Sequencing was done on an Illumina NovaSeq 6000 sequencer. The pooled libraries were sequenced on one lane of an S-Prime flow cell at 50bp paired-end.  Sequencing was done on an Illumina NovaSeq 6000 sequencer.  The pooled libraries were sequenced on one lane of an S-Prime flow cell at 50bp paired-end.  Once generated, sequence data was demultiplexed and Fastq files generated using bcl2fastq v2.20.0.422 file converter from Illumina.

treatment_protocol: Mice were injected with tamoxifen dissolved in corn oil intraperitoneally four times every other day at 6-8 weeks of age. Seven days later mice were humanely euthanized.

tag: genotype

value: LSL-KrascomQ61R/+; Rosa26Cre-ERT2/+

value: Tamoxifen

value: lung

value: M


title: RM5_CD4_RNASeq

organism: Macaca mulatta


title: T177676


title: Input_PCIF1 KO_HIV_rep2

description: Group 4_KO_HIV_pri.csv


title: T179223


title: T179483


title: cells sampling at week 8_1 [Hashtag]

description:
w8_1_rawdata
w8_1_anno


title: Input_PCIF1 KO_HIV_rep1

description: Group 4_KO_HIV_pri.csv


title: RM4_CD4_RNASeq


title: ComQ61R_2

value: F


title: Input_PCIF1 KO_mock_rep3

description: Group 3_KO_mock_pri.csv


title: cells sampling at week 12_1

description:
w12_1_rawdata
w12_1_anno


title: Input_PCIF1 KO_mock_rep1

description: Group 3_KO_mock_pri.csv


title: Input_control_HIV_rep3

description: Group 2_HIV_pri.csv


title: cells sampling at week 10_2

description:
w10_2_rawdata
w10_2_anno


title: T181549


title: ComG12D_1

value: LSL-KrascomG12D/+; Rosa26Cre-ERT2/+


title: ComG12D_2


title: cells sampling at week 10_1

description:
w10_1_rawdata
w10_1_anno


title: Input_control_HIV_rep2

description: Group 2_HIV_pri.csv


title: Input_PCIF1 KO_mock_rep2

description: Group 3_KO_mock_pri.csv


title: cells sampling at week 12_2

description:
w12_2_rawdata
w12_2_anno


title: NatQ61R_1

value: LSL-KrasnatQ61R/+; Rosa26Cre-ERT2/+


title: ComQ61R_1


title: Input_control_HIV_rep1

description: Group 2_HIV_pri.csv


title: M2 135 (A375) 24H

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

data_processing:
DNBseq platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene ID and FPKM values for each sample

source_name: M2 macrophages cocultured with A375 cells for 24 hours

growth_protocol:
For in vitro generation of M2 macrophages, monocytes were incubated with 10 ng/mL M-CSF for 7 days renewing cytokines every 3 days. Macrophages were cocultured with A375 cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA purification kit from Macherey-Nagel
RNA libraries were prepared for sequencing using standard BGI protocols

value: Monocyte-derived M-CSF macrophages


title: cells sampling at week 8_2

description:
w8_2_rawdata
w8_2_anno


title: NatQ61R_2


title: ComG12D_3


title: NatQ61R_3


title: NatG12D_2

value: LSL-KrasnatG12D/+; Rosa26Cre-ERT2/+


title: M2 135 (BLM) 24H

source_name: M2 macrophages cocultured with BLM cells for 24 hours

growth_protocol:
For in vitro generation of M2 macrophages, monocytes were incubated with 10 ng/mL M-CSF for 7 days renewing cytokines every 3 days. Macrophages were cocultured with BLM cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: M2 134 (BLM) 24H


title: Input_control_mock_rep2

description: Group 1_control_pri.csv


title: M2 133 (A375) 24H


title: Input_control_mock_rep3

description: Group 1_control_pri.csv


title: Input_control_mock_rep1

description: Group 1_control_pri.csv


title: NatG12D_3


title: M2 134 (A375) 24H


title: NatG12D_1


title: ComQ61R 3

data_processing:
RNA-seq data was processed using the TrimGalore toolkit, which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20 nucleotides or longer after trimming were kept for further analysis.  Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.  Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Gene set enrichment analysis was performed to identify gene ontology terms and pathways associated with altered gene expression for each of the comparisons performed.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: matrix table includes raw gene counts for every gene and every sample and their differential expression in KrasComQ61R with respect to the KrasNatG12D allele.
Supplementary_files_format_and_content: matrix table includes GSEA enrichment of HALLMARKS in KrasComQ61R with respect to the KrasNatG12D allele.


title: cells sampling at week 8_1

description:
w8_1_rawdata
w8_1_anno


title: GRWRI3_L8_mock_rep1

city: Davis

first: Michelle

last: Tang

address: One Shields Avenue

department: Plant Sciences

institute: UC Davis

data_processing:
Before and after read processing, libraries were analyzed with FastQC v.0.11.7.
Barcodes trimmed using TrimGalore v0.6.0 using default settings.
PolyA were trimmed using TrimGalore v0.6.0 (--polyA)
Trimmed reads were mapped to the Arabidopsis thalian reference genome (TAIR10) and raw read counts were obtained using STAR aligner v2.7.0f
Genome_build: Arabidopsis thaliana TAIR v10
Supplementary_files_format_and_content: tab delimited txt file containing raw counts

organism: Arabidopsis thaliana

source_name: pooled whole seedlings

growth_protocol: 200-300 seeds per plate were sown in a line on nylon mesh on 100 x 100 mm petri dish with half-strength Murashige and Skoog and stratified at 4 C for two nights. Double foil wrapped plates were then transferred to a dark chamber at ambient room temperature (20-23 C) and allowed to grow for 5 days.

extract_protocol:
Whole seedlings from one plate constitutes a biological replicate. Whole seedlings were collected and flash frozen in liquid nitrogen and stored in -80C until direct mRNA extraction following the protocol from Townsley et al. 2015. Collection was performed in the dark assisted with a green headlamp.
RNA-Seq libraries were prepared following the high-throughput protocol from Kumar et al. 2014.

treatment_protocol: After 5 days, plates were unwrapped in the dark and nylon mesh with seedlings were transferred onto fresh half-strength MS plates containing 10 uM dexamethasone or mock plates for 24 hours.

tag: allele

value: Mock

tag: replicate


title: M2 135 24H

source_name: M2 macrophages

growth_protocol:
For in vitro generation of M2 macrophages, monocytes were incubated with 10 ng/mL M-CSF for 7 days renewing cytokines every 3 days.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: WT_3

value: WT

value: 129S6; Rosa26Cre-ERT2/+


title: 15308X1 Day 21 post-infection

city: Irvine

first: Thomas

last: Lane

address: Ring Rd.

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 2.2.0 to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-1.2.0 reference from 10X Genomics.
Barcodes and UMIs were counted using cellranger count with expected-cells=3000
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: CD45+ CNS infiltrating immune cells and microglia

extract_protocol:
Tissue was extracted from isofluorine euthanized mice after saline cardiac perfusion. Single cell suspensions were generated from tissue samples by grinding with frosted microscope slides. Immune cells were then enriched via a 2-step Percoll cushion (90% and 63%) and cells were collected at the interface of the two Percoll layers. These cells were then FACS sorted for CD45+ using CD45-APC conjugated Flow antibodies.
Single-cell 3' RNA-Sequencing

value: Spinal Cord

tag: timepoint

value: Day 21 post-infection


title: GRWRI3_L8_mock_rep2


title: 15307X1 Day 3 post-infection

value: Brain

value: Day 3 post-infection


title: WT_2


title: M2 133 (BLM) 24H


title: 15307X2 Day 7 post-infection

value: Day 7 post-infection


title: 15442X1 Uninfected Control

value: Uninfected


title: GRWRI3_L21_mock_rep2


title: ComQ61R 1

value: LSL-KrascomQ61R/+; Rosa26Cre-ERT2/+

value: Tamoxifen


title: M2 134 24H


title: WT_1

value: lung

value: M


title: ComQ61R 2


title: M1 135 (SK103) 24H

source_name: M1 macrophages cocultured with SKMEL103 cells for 24 hours

growth_protocol:
For in vitro generation of M1 macrophages, monocytes were incubated with 1000 U/ml GM-CSF for 7 days renewing cytokines every 3 days. Macrophages were cocultured with SKEML103 cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).

value: Monocyte-derived GM-CSF macrophages


title: M2 133 24H


title: GRWRI3_L21_mock_rep1


title: GRWRI3_L8_dex_rep2

value: 10 uM Dexamethasone


title: M1 133 (SK103) 24H


title: NatG12D 3


title: GRWRI3_L8_dex_rep1


title: DCIS_IgG_rep2

city: Watervliet

first: Ali

middle: Salman

last: Ropri

address: 12 Lakeshore Dr., Apt 1B

department: Biomedical Sciences

institute: SUNY Albany

data_processing:
 Quality of samples for ChIP were assessed using the Bioconductor package FastQC (version 0.11.9)
Data was mapped to the human reference genome (hg38 assembly) using STAR Aligner (version 2.7.0)
PCR duplicated reads were filtered using Sambamba (version 0.7.1)
The MACS2 (version 2.2.7.1) algorithm was used to identify enriched regions (peaks). Default parameters were used except to ensure broad regions were identified; broad peak calling was used with a broad cutoff of 0.1. Reads were normalized to mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: Epithelial Cells

growth_protocol: MCF10A, MCF10A-AT1, DCIS.com, and MCF10A-CA1 cells were grown to a final count of 5 x 10^6. The cells were maintained in a culture of Dulbecco's modified Eagle's medium (DMEM) medium supplemented with 5% horse serum, 20 ng/mL EGF, 0.5 mg/mL hydrocortisone, 100 ng/mL cholera toxin, 10 μg/mL insulin and 1× antibiotic‐antimycotic (Gibco, Grand Island, NY)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
1 to 10 ng of DNA was prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit (E7645S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (E7335S)

value: DCIS

value: Breast; Mammary gland

value: ductal carcinoma in situ

value: epithelial cells

value: IgG- Cell Signaling(Rabbit (DA1E) mAb IgG XP® Isotype Control #3900

value: Untreated


title: DCIS_IgG_rep1


title: M1 134 (SK103) 24H


title: NatG12D 2

value: LSL-KrasnatG12D/+; Rosa26Cre-ERT2/+

value: F


title: GRWRI3_L21_dex_rep1


title: GRWRI3_L17_mock_rep2

value: Mock


title: GRWRI3_L17_mock_rep1


title: DCIS_H3K_rep1

value: H3K27ac (abcam ChIP Grade (ab4729))


title: M1 133 (A375) 24H

source_name: M1 macrophages cocultured with A375 cells for 24 hours

growth_protocol:
For in vitro generation of M1 macrophages, monocytes were incubated with 1000 U/ml GM-CSF for 7 days renewing cytokines every 3 days. Macrophages were cocultured with A375 cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: M1 134 (A375) 24H


title: GRWRI3_L17_dex_rep2


title: SPF4

city: Marburg

first: Rossana

last: Romero

state: Hessen

address: Hans Meerwein Str. 2D

department: Institute of medical microbiology

institute: Philipps University Marburg

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastq-mcf program (v1.05) and cutadapt (v2.5), unwanted sequences include: mitochondrial genome sequences, ribosomal RNAs, transfer RNAs were removed using Bowtie2 (v2.5.1). Filtred reads were mapped to Mouse GRCm38 genome using STAR v2.7.3a with default parameters. The aligned reads were used for estimating expression of the genes. The raw read counts were estimated using HTSeq (v0.11.2). Read count data were normalized using DESeq2. Additionally the aligned reads are used for estimating expression of the genes using cufflinks (v2.2.1). The expression values are reported in FPKM (Fragments per kilobase per million) units for each gene. Differential expression analysis was performed using DESeq2 (R Bioconductor package). Over Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA) and Pathway analysis was performed for significantly differentially expressed up and down regulated protein coding genes.
tab-delimited text files include raw and normalized counts for each Sample ...
Genome_build: Mouse (GRCm38)
Supplementary_files_format_and_content: Raw and Normalized Count Matrix

source_name: SPF_whole colon

extract_protocol:
Whole colon (10mg±2mg) was removed and store in Allprotect tissue reagent. RNA was isolated using Allprep DNA/RNA/Protein kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: strain background

tag: sample group

value: SPF


title: NatG12D 1

value: Tamoxifen

tag: tissue


title: SPF1


title: SPF3


title: M1 133 (BLM) 24H

source_name: M1 macrophages cocultured with BLM cells for 24 hours

growth_protocol:
For in vitro generation of M1 macrophages, monocytes were incubated with 1000 U/ml GM-CSF for 7 days renewing cytokines every 3 days. Macrophages were cocultured with BLM cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: GRWRI3_L10_mock_rep2


title: M1 135 24H

source_name: M1 macrophages

growth_protocol:
For in vitro generation of M1 macrophages, monocytes were incubated with 1000 U/ml GM-CSF for 7 days renewing cytokines every 3 days.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: M1 135 (A375) 24H


title: DCIS_H3K_rep2

tag: chip antibody


title: GRWRI3_L17_dex_rep1


title: GRWRI3_L10_dex_rep2


title: SPF2


title: M1 134 24H


title: M1 134 (BLM) 24H


title: OMM+MC2_3_D8

source_name: OMM+MC2_D8_whole colon


title: OMM+MC2_2_D8


title: Mo 135 (A375) 24H

source_name: Monocytes cocultured with A375 cells for 24 hours

growth_protocol:
Monocytes were cocultured with A375 cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).

value: Monocytes CD14+


title: GRWRI3_L10_dex_rep1


title: GRWRI3_L10_mock_rep1


title: GRLBD16_L8_mock_rep1


title: OMM+MC2_4_D8


title: OMM+MC2_2_D6

source_name: OMM+MC2_D6_whole colon


title: GRLBD16_L8_dex_rep2


title: GRWRI3_L21_dex_rep2


title: M1 135 (BLM) 24H


title: M1 133 24H


title: OMM+MC2_1_D8


title: GRLBD16_L8_dex_rep1


title: Mo 135 (BLM) 24H

source_name: Monocytes cocultured with BLM cells for 24 hours

growth_protocol:
Monocytes were cocultured with BLM cells for 24 hours and separated with CD14 microbeads.
Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: OMM+MC2_4_D6


title: OMM+MC2_4_D4

source_name: OMM+MC2_D4_whole colon


title: MCF7_E2-EHT10uM_rep1

city: Miami

first: Jun

last: Sun

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Base calling using Illumina BCL2fastq v2.19.0.316
Trimmed fastq files with cutadapt v.1.18  --a AGATCGGAAGAGCACACGTC -m 30
Aligned to the hg19 genome assembly using tophat2 1.0 with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bw file was generated by deeptools 3.1.1 that was normalized to CPM.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured with 5% FBS in IMEM and switched to IMEM with 5% charcoal-treated FBS for 3 days before the treatment.

extract_protocol:
Total RNA was extracted after 3 days using TRIzol (Invitrogen).
The purified RNA samples were subjected to library preparation using NEBNext Ultra II Directional RNA Library Pep Kit (New England Biolabs #E7760).

treatment_protocol: MCF-7 cells were treated for 1 h in the presence of 2mM BrU.

value: Breast cancer cell line

value: E2-EHT 10uM


title: MCF7_E2-EHT5uM_rep2

value: E2-EHT 5uM


title: Mo 134 (BLM) 24H


title: Mo 133 (A375) 24H


title: GRLBD16_L3_mock_rep2


title: OMM+MC2_1_D6


title: MCF7_E2-EHT5uM_rep1


title: GRLBD16_L8_mock_rep2


title: Mo 133 (BLM) 24H


title: OMM+MC2_3_D4


title: MCF7_E2-EHT10uM_rep2


title: GRLBD16_L3_mock_rep1


title: Mo 135 24H

source_name: Monocytes from healthy donors peripheral blood

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).


title: MCF7_E2-EHT2uM_rep2

value: E2-EHT 2uM


title: Mo 134 24H


title: Mo 133 24H


title: GRLBD16_L3_dex_rep1

value: 10 uM Dexamethasone


title: MCF7_control_rep1

value: control


title: MCF7_E2-EHT2uM_rep1


title: GRLBD16_L12_mock_rep2


title: OMM+MC2_2_D4


title: T180389

source_name: ICC

value: intrahepatic cholangiocarcinoma

value: liver

value: ICC

value: male


title: OMM+MC2_2_D2

source_name: OMM+MC2_D2_whole colon


title: MCF7_siRAC1_rep2

growth_protocol: MCF-7 cells were cultured with 5% FBS in IMEM.

extract_protocol:
Total RNA was extracted after 3 days using TRIzol (Invitrogen).
Ribosomal RNA was removed using the NEBNext rRNA Depletion kit (New England Biolabs #E6310). RNA library was prepared using NEBNext Ultra II Directional RNA Library Pep Kit (New England Biolabs #E7760).

treatment_protocol: MCF-7 cells were transfected with control siRNA or siRNA targeting RAC1 using RNAiMAX (Invitrogen).

tag: transfection


title: GRLBD16_L12_mock_rep1

source_name: pooled whole seedlings


title: GRLBD16_L11_mock_rep2


title: OMM+MC2_1_D4


title: GRLBD16_L3_dex_rep2


title: TAM 279

source_name: Macrophages isolated from human melanoma

value: Tumor Associated Macrophages CD14+

value: Skin melanoma


title: OMM+MC2_3_D6


title: GRLBD16_L11_mock_rep1

value: Mock


title: MCF7_E2_rep2


title: Mo 134 (A375) 24H


title: MCF7_E2_rep1


title: MCF7_siControl_rep1

value: siControl


title: GRLBD16_L12_dex_rep2


title: TAM 285


title: GRLBD16_L12_dex_rep1


title: GRLBD16_L11_dex_rep1


title: OMM2

source_name: OMM_whole colon

value: colon

value: OMM


title: OMM+MC2_1_D2


title: Mo 276

source_name: Monocytes from melanomas patients peripheral blood

value: Monocytes CD14+


title: OMM+MC2_4_D2


title: TAM 275


title: OMM3


title: MCF7_siRAC1_rep1

value: Breast cancer cell line


title: TAM 274


title: Mo 279


title: OMM+MC2_3_D2


title: Mo 275


title: TAM 278


title: OMM4


title: GRENAP1_L5_mock_rep1


title: MCF-7 MCF-7 input DNA

description:
MCF-7 input DNA
MCF-7

data_processing:
Base calling using Illumina BCL2fastq v2.19.0.316
Trimmed fastq files with cutadapt v.1.18  --a AGATCGGAAGAGCACACGTC -m 30
Aligned to the hg19 genome assembly using bowtie2 2.2.6 with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bw file was generated by deeptools 3.1.1 that was normalized to CPM.

growth_protocol: MCF-7 cells were cultured with 5% FBS in IMEM. MDA-MB-231 cells were cultured with 10% FBS in DMEM.

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min at RT. Sonicated nuclear lysates were used in immunoprecipitation with a target antibody.
Libraries were prepared using NEBNext UltraII DNA library Kit for Illumina (E7645).

treatment_protocol: MCF-7 cells were switched to IMEM containing 5% charcoal-treated FBS for 3 days before treating the cells for 45 min with 10 nM E2, 50 µM EHT 1864 or combination.


title: MCF7_siControl_rep2


title: GRLBD16_L11_dex_rep2


title: OMM1


title: Knockout sample B

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
Separately, SAMtools (version 1.9) was used to count reads aligning in proper pairs at least once to either strand of the mitochondrial chromosome (chrM) or to the sense or antisense strands of Ensembl loci of gene biotype "rRNA" or of non-mitochondrial RepeatMasker loci of class "rRNA" (as defined in the RepeatMasker track retrieved from the UCSC Table Browser).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.23.10).
Genome_build: mm10
Supplementary_files_format_and_content: counts, VST

source_name: Flow-sorted Scgb1a1 lineage traced lung epithelial cells

growth_protocol: Cells were isolated by FACS from collagenase-digested mouse lungs and directly processed for RNA isolation.

extract_protocol:
Cells were lysed in TRIzol for RNA extraction.
The libraries were prepared from 100-200 ng total RNA enriched for mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (New England Biolabs, USA) and sequenced on an Illumina NextSeq 2000 instrument at 650 pM (Illumina, USA).

treatment_protocol: Mice were dosed with tamoxifen by intraperitoneal injection for 5 consecutive days. Lungs were collected on day 12 following onset of administration.

value: Yap1/Wwtr1 knockout


title: MCF7_control_rep2


title: MDA-MB-231ER MDA-MB-231ER input DNA

description:
MDA-MB-231ER input DNA
MDA-MB-231ER

source_name: MDA-MB-231ER cells


title: MDA-MB-231 MDA-MB-231 input DNA

description:
MDA-MB-231 input DNA
MDA-MB-231

source_name: MDA-MB-231 cells


title: GRENAP1_L5_dex_rep1


title: GF4

source_name: GF_whole colon

value: GF


title: GRENAP1_L5_dex_rep2


title: MDA-MB-231ER RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MDA-MB-231ER

value: RAC1 (Millipore, 05-389)


title: MDA-MB-231ER RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MDA-MB-231ER


title: GF3


title: GRENAP1_L5_mock_rep2


title: GRENAP1_L4_mock_rep1


title: MCF-7 C4-12 MCF-7 C4-12 input DNA

description:
MCF-7 C4-12 input DNA
MCF-7 C4-12

source_name: MCF-7 C4-12 cells


title: Knockout sample A


title: Knockout sample C


title: Control sample C

value: Control


title: aGVHD

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

data_processing:
FastQC0.11.3 to perform basic statistics on the quality of the raw reads
celltanger3.1.0 count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline  using default parameters
All downstream single-cell analyses were performed using Cell Ranger and Seurat  ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically
Subsequent analysis of cellranger reanalyze and Seurat were all performed basing on this output gene expression matrix
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow niche cells

growth_protocol: Cells were directly isolated from mice.

extract_protocol:
We isolated stromal cells from mice by fluorescence activated cell sorting (FACS) after labeling CD45, lineage mix, and CD71 to deplete hematopoietic cells, and Calcein AM and DAPI to eliminate the dead cells
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT group was no treated female wild type(WT) CB6F1 mice (named 'NC' in article). 5x106 BM nucleated cells (BMNCs) from B6.SJL mice (CD45.1+) were intravenously injected into female CB6F1 recipients (CD45.2+) 4 hours after sub-lethal- irradiation (4.0 Gy, twice) to establish the BMT model. Additional spleen cells (6x107) from female C57BL/6 mice were injected into the BMT mice to establish the aGVHD model.

value: Bone marrow niche cells

tag: strain

value: bone marrow transplantation and splenic cell infusion (to develop aGVHD)


title: GF1


title: GRENAP1_L4_mock_rep2


title: GF2


title: Bone marrow transplantation

tag: cell type

value: bone marrow transplantation


title: Control sample B


title: WT

tag: treatment

value: untreated


title: Shade_28C_rep3

city: CABA

first: Carlos

middle: Esteban

last: Hernando

state: Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description:
Total RNA was extracted from whole seedlings
gene_counts_voom.txt

data_processing:
Base-calling by default setting of Illumina HiSeq 1500
Aligment to to Arabidopsis thaliana TAIR10 genome using TopHat v2.1.1
Generation of BAM files with SAMtools V1.3
Data analysis with Voom function using R 4.0.2
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: All processed data files are .txt count tables containing the number of raw counts in each sample for all the sequenced gene trasncripts of Arabidopsis thaliana genome.

source_name: seedlings

growth_protocol: Seeds of Arabidopsis thaliana were sown on 0.8 % agar-water in Petri dishes, stratified 5-7 d at 5 ºC in darkness and transferred to a growth room at 22°C with a photoperiod of 10 h of 100 μmolm −2 s −1 of white light (400–700 nm) provided by a mixture of fluorescent and halogen lamps (red/far-red ratio = 1.1).

extract_protocol:
In the transcriptional profiling assay total RNA was extracted with Spectrum™ Plant Total RNA Kit (Sigma) following the manufacturer’s protocols.
Libraries were prepared following the TrueSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, first-strand cDNA synthesized by reverse transcriptase (SuperScript III; Invitrogen) using random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies). Samples were pooled to create 12 multiplexed DNA libraries, which were pair-end sequenced with an Illumina HiSeq1500.

treatment_protocol: Three day old seedlings of the wild type Columbia were exposed during the photoperiod of day 4 (10 h) to white light at 20C, white light at 28C, shade at 20C or shade at 28C. Samples were collected at the end of the day 4.

value: exposed during the photoperiod of day 4 (10 h) to shade at 28C.

value: wild-type Columbia 0

tag: life stage

value: Three day old seedlings


title: Control sample A


title: MDA-MB-231ER ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MDA-MB-231ER

value: ER (Santa Cruz, sc543)


title: MDA-MB-231 RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MDA-MB-231


title: RNA sequencing from Whole mice brain RNA_C57BL/6 IRF8-/- JEV #11

city: Faridabad

first: Arup

last: Banerjee

state: Haryana

address: NCR Biotech Science Cluster

country: India

institute: Regional Centre for Biotechnology

data_processing:
The raw reads corresponding to Illumina RNA-seq FASTQ files were aligned in Strand NGS software v3.4 against the Mouse reference genome (Build mm10, Gene feature: Ensembl Genes, Library layout: Paired end).
Quantification was done to obtain the read densities by Strand NGS software.
Differential expression analysis of mRNA from different groups was performed using the DESeq script 2 via the script editor in Strand NGS with a p-value ≤ 0.05 and fold change 2.0 fold.
Genome_build: Mouse reference genome (Build mm10, Gene feature: Ensembl Genes, Library layout: Paired end)

source_name: C57BL/6 IRF8-/- JEV #11_mice brain

growth_protocol: C57BL/6 WT and Irf8-/- mice (3-4 weeks) were maintained at the small animal facilities. Mice have housed in HEPA filter-top cages under class II biohazard conditions, with food and water provided ad libitum.

extract_protocol:
Mice were sacrificed 24 hour post to symptom onset followed by transcardial perfusion with ice-cold 1xPBS, brains were harvested and Total RNA was extracted using the RNeasy kit with on-column DNAse treatment, (74004; QIAGEN) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent TapeStation (Agilent, Palo Alto, CA, USA) and RNA concentration was quantified by Qubit 4.0 spectrophotometer. Total RNA was used as the input material for ribosomal RNA depletion and RNA sequencing library preparation.
The library was prepared for sequencing using the TruSeq standard total RNA library preparation kit (Illumina, San Diego, CA, USA). The resulting cDNA libraries were quantified using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA, USA), and quality and size were checked using the Agilent High Sensitivity DNA Kit.
Each sample was prepared using 300 ng of total RNA. The average fragment length of the cDNA libraries was 330 bp. RNA-seq libraries were sequenced using paired-end 100 bases (PE100) sequencing chemistry on Novaseq instruments following the manufacturer’s protocols (Illumina). samples ran on four lane (L1-L4) and pair end sequence (R1 & R2)

treatment_protocol: Mice (WT, Irf8-/-) of either sex were randomly divided into two groups. Mice (n=5) in the infection group were inoculated through the intraperitoneal (i.p) route with 1x107 plaque forming unit (pfu)/100ul of JEV while mice (n=5) in the mock-infected group received an equal volume of sterile Eagle’s Minimal Essential Medium (MEM, Invitrogen, Carlsbad, CA, USA) by the same route. Mice were weighed and observed untill they developed viral encephalitis/clinical symptoms.

tag: agent

value: JEV


title: GRENAP1_L4_dex_rep1

growth_protocol: 200-300 seeds per plate were sown in a line on nylon mesh on 100 x 100 mm petri dish with half-strength Murashige and Skoog and stratified at 4 C for two nights. Double foil wrapped plates were then transferred to a dark chamber at ambient room temperature (20-23 C) and allowed to grow for 5 days.

value: 10 uM Dexamethasone


title: RNA sequencing from Whole mice brain RNA_C57BL/6 IRF8-/- JEV #10

source_name: C57BL/6 IRF8-/- JEV #10_mice brain


title: MDA-MB-231ER ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MDA-MB-231ER


title: GRENAP1_L2_mock_rep2

value: Mock


title: MDA-MB-231 ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MDA-MB-231


title: Shade_28C_rep2


title: RNA sequencing from Whole mice brain RNA_C57BL/6 IRF8-/- JEV #9

source_name: C57BL/6 IRF8-/- JEV #9_mice brain


title: Shade_28C_rep1


title: MDA-MB-231 RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MDA-MB-231


title: GRENAP1_L2_dex_rep2


title: Shade_20C_rep2

value: exposed during the photoperiod of day 4 (10 h) to shade at 20C.


title: GRENAP1_L1_mock_rep2


title: GRENAP1_L2_mock_rep1


title: GRENAP1_L4_dex_rep2


title: RNA sequencing from Whole mice brain RNA_C57BL/6 IRF8-/- mock #7

source_name: C57BL/6 IRF8-/- mock #7_mice brain


title: RNA sequencing from Whole mice brain RNA_C57BL/6 WT-JEV #5

source_name: C57BL/6 WT-JEV #5_mice brain

value: WT


title: MCF-7 C4-12 RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF-7 C4-12

value: Breast cancer cell line


title: MDA-MB-231 ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MDA-MB-231


title: MCF-7 C4-12 RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MCF-7 C4-12


title: RNA sequencing from Whole mice brain RNA_C57BL/6 IRF8-/- mock #8

source_name: C57BL/6 IRF8-/- mock #8_mice brain


title: GRENAP1_L1_mock_rep1

source_name: pooled whole seedlings


title: Shade_20C_rep1


title: RNA sequencing from Whole mice brain RNA_C57BL/6 WT-JEV #6

source_name: C57BL/6 WT-JEV #6_mice brain


title: MCF7_DHT RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MCF7_DHT

source_name: MCF-7 cells


title: GRENAP1_L2_dex_rep1


title: RNA sequencing from Whole mice brain RNA_C57BL/6 WT-JEV #4

source_name: C57BL/6 WT-JEV #4_mice brain


title: MCF7_DHT RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF7_DHT


title: Shade_20C_rep3


title: Light_28C_rep2

value: exposed during the photoperiod of day 4 (10 h) to white light at 28C.


title: Light_28C_rep1


title: Light_28C_rep3


title: RNA sequencing from Whole mice brain RNA_C57BL/6 WT-mock #1

source_name: C57BL/6 WT-mock #1_mice brain


title: GRENAP1_L1_dex_rep1


title: GRCHA19_L9_mock_rep1


title: RF4_CD14_RNASeq

source_name: Primary CD14+ monocytes from PBMCs

tag: Sex

value: Female


title: Light_20C_rep3

value: exposed during the photoperiod of day 4 (10 h) to white light at 20C.


title: GRCHA19_L9_dex_rep2


title: MCF-7_E2-EHT RNA Pol II_ChIPSeq rep2

description:
RNA Pol II_ChIPSeq rep2
MCF-7_E2-EHT

value: RNA PolII (Santa Cruz, sc-899)


title: GRCHA19_L9_mock_rep2


title: Light_20C_rep2


title: Light_20C_rep1


title: MCF7_DHT AR_ChIPSeq rep2

description:
AR_ChIPSeq rep2
MCF7_DHT

value: AR (Millipore, 06-680 )


title: RNA sequencing from Whole mice brain RNA_C57BL/6 WT-mock #2

source_name: C57BL/6 WT-mock #2_mice brain


title: GRENAP1_L1_dex_rep2


title: T1D_6414

city: Gainesville

first: Alberto

last: Riva

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Quality control performed with fastqc and trimmomatic.
Reads mapped to human genome reference using Bowtie2.
Gene expression quantified with RSEM.
A multi-dimensional scaling (MDS) plot was used to detect outlier samples before differential gene expression analysis.
Empirical Bayes techniques were implemented using limma voom in R to identify differentially expressed genes between donor groups.
Network analysis and functional enrichment were performed using Ingenuity Pathway Analysis (IPA) software.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq-counts.xlsx: Excel table containing raw counts for all genes in all samples.
Supplementary_files_format_and_content: AAb-ND_core_analysis.xls: Results of IPA (pathway) analysis on differentially expressed genes in Aab vs ND
Supplementary_files_format_and_content: AAb-T1D_core_analysis.xls: Results of IPA (pathway) analysis on differentially expressed genes in Aab vs T1D

source_name: laser microdissected islets

extract_protocol:
PicoPure RNA extraction kit (Thermofisher Scientific, cat# 12204-01) with genomic DNA removal using recombinant DNAse1 (Worthington Biochemical Corporation, cat# LS006361)
Agilent 2100 Bioanalyzer (Picotape, Agilent Technologies)
A sample of 6 ng RNA was used to extract mRNA with 15μl of NEBNext Magnetic Oligo d(T) and fragmented in NEBNext First Strand Synthesis Buffer by heating at 94°C for 8 minutes in a 96-well plate. First strand cDNA synthesis was performed using reverse transcriptase and random primers. Synthesis of double-stranded (ds) cDNA was performed using the second strand master mix provided in the kit. The resulting ds cDNA was end-repaired, dA-tailed, and ligated with NEBNext adaptors. The library was enriched by PCR amplification and purified by Agencourt AMPure beads (Beckman Coulter). Barcoded libraries were sized on the Bioanalyzer and quantitated by QUBIT. The library's functionality was validated by quantitative reverse transcription PCR (qRT-PCR), using the KAPA library quantification kit (Kapa Biosystems).

value: laser microdissected islets

tag: disease state

value: diabetic

tag: biorep


title: GRCHA19_L8_mock_rep2


title: MCF7_DHT AR_ChIPSeq rep1

description:
AR_ChIPSeq rep1
MCF7_DHT


title: MCF-7_EHT RNA Pol II_ChIPSeq rep1

description:
RNA Pol II_ChIPSeq rep1
MCF-7_EHT


title: MCF-7_EHT RNA Pol II_ChIPSeq rep2

description:
RNA Pol II_ChIPSeq rep2
MCF-7_EHT


title: RM2_CD14_RNASeq

data_processing:
Data was processed using the Salmon pipeline (version 0.14.1), [PMID: 28263959].
Genome_build: rhemac10 (samples 1-5) papanu4 (samples 6-9)
Supplementary_files_format_and_content: The quant.sf file provides TPM for each NCBI transcript.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Male


title: MCF-7_E2 RNA Pol II_ChIPSeq rep1

description:
RNA Pol II_ChIPSeq rep1
MCF-7_E2

value: 10 nM E2


title: GRCHA19_L8_dex_rep2


title: MCF-7_control RNA Pol II_ChIPSeq rep2

description:
RNA Pol II_ChIPSeq rep2
MCF-7_control

value: control


title: GRCHA19_L8_dex_rep1


title: RM4_CD14_RNASeq


title: T1D_6306


title: MCF-7_control RNA Pol II_ChIPSeq rep1

description:
RNA Pol II_ChIPSeq rep1
MCF-7_control


title: GRCHA19_L7_mock_rep2


title: GRCHA19_L9_dex_rep1


title: T1D_6362


title: T1D_6228


title: GRCHA19_L7_mock_rep1


title: RNAseq_0SPD_rep2

city: Bethesda

last: Dever

address: BG 6 RM 228 6 CENTER DR

department: NICHD

institute: National Institutes of Health

data_processing:
Fastq files were processed as described in McGlincy et al. Methods (2017) 126: 112–129. Briefly, fastq sequences were trimmed with cutadapt to remove constant adapter sequences (AGATCGGAAGAGCAC). For each sample set, mixed fastq reads were separated based on the sample barcodes. Non-coding RNA (ncRNA) sequences were removed by aligning each fastq file against reference ncRNA (downloaded from https://useast.ensembl.org/) using Bowtie (1.2.2), and the nonaligned reads were used for further analysis. After removing the PCR duplicates by custom python (3.7) script, final reads were mapped to R64-1-1 S288C SacCer3 transcriptome using bowtie (1.1.2), generating sam files. Read counts obtained from sam files were analyzed in 0 µM SPD vs 10 µM SPD conditions for TE analysis using Riborex-edgeR.
Translational efficiency change analysis was performed with Riborex-edgeR.
Genome_build: R64-1-1 S288C SacCer3
Supplementary_files_format_and_content: Reads_TE_spd0_spd10uM.xlsx: Excel file includes raw read count table for each sample. Total 9 columns: column A: ORF Name and columns B to I showing raw read counts for each sample; column B: RNAseq_0SPD_rep1; column C: RNAseq_0SPD_rep2; column D: RNAseq_10uMSPD_rep1; column E: RNAseq_10uMSPD_rep2; column F: riboseq_0SPD_rep1; column G: riboseq_0SPD_rep2; column H: riboseq_10uMSPD_rep1; and column I: riboseq_10uMSPD_rep2

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Yeast cells grown to OD600 0.6-0.7 from starting OD 0.025 at 30 degrees in SD medium with 0 added SPD.

extract_protocol: For RNaseq library preparation, 10 µg total RNA was incubated in Ambion Fragmentation Reagent at 70 °C for 15 min, and the reaction was stopped by adding Stop Solution (ThermoFisher). Fragments were separated by electrophoresis on a 15% polyacrylamide TBE-Urea gel; after column purification and precipitation, RNA fragments were processed for cDNA library preparation as described above for RiboSeq.

treatment_protocol: No treatment.

tag: genotype

value: MATa ura3-52 leu2 spel D::LEU2 spe2 D::LEU2

tag: condition

value: 0uM SPD


title: MCF-7_E2-EHT RNA Pol II_ChIPSeq rep1

description:
RNA Pol II_ChIPSeq rep1
MCF-7_E2-EHT


title: riboseq_0SPD_rep2

description: Ribosome-protected RNA 17-34 nt

data_processing:
Library strategy: Ribo-Seq
Fastq files were processed as described in McGlincy et al. Methods (2017) 126: 112–129. Briefly, fastq sequences were trimmed with cutadapt to remove constant adapter sequences (AGATCGGAAGAGCAC). For each sample set, mixed fastq reads were separated based on the sample barcodes. Non-coding RNA (ncRNA) sequences were removed by aligning each fastq file against reference ncRNA (downloaded from https://useast.ensembl.org/) using Bowtie (1.2.2), and the nonaligned reads were used for further analysis. After removing the PCR duplicates by custom python (3.7) script, final reads were mapped to R64-1-1 S288C SacCer3 transcriptome using bowtie (1.1.2), generating sam files. Read counts obtained from sam files were analyzed in 0 µM SPD vs 10 µM SPD conditions for TE analysis using Riborex-edgeR.
Translational efficiency change analysis was performed with Riborex-edgeR.
Genome_build: R64-1-1 S288C SacCer3
Supplementary_files_format_and_content: Reads_TE_spd0_spd10uM.xlsx: Excel file includes raw read count table for each sample. Total 9 columns: column A: ORF Name and columns B to I showing raw read counts for each sample; column B: RNAseq_0SPD_rep1; column C: RNAseq_0SPD_rep2; column D: RNAseq_10uMSPD_rep1; column E: RNAseq_10uMSPD_rep2; column F: riboseq_0SPD_rep1; column G: riboseq_0SPD_rep2; column H: riboseq_10uMSPD_rep1; and column I: riboseq_10uMSPD_rep2

extract_protocol: Ribosome profiling (Cell filteration, Freeze-Mill lysis, RNase I footprinting, size selection, RNA extraction, preadenylated linker ligation, sample pooling, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Transcriptome-wide measurement of translation by ribosome profiling" Nicholas J. McGlincy et al. Methods. 2017 August 15; 126: 112–129. doi:10.1016/j.ymeth.2017.05.028.


title: MCF-7_E2 RNA Pol II_ChIPSeq rep2

description:
RNA Pol II_ChIPSeq rep2
MCF-7_E2


title: RNAseq_0SPD_rep1


title: T1D_6342


title: T1D_6371


title: ND_6401

value: control non-diabetic


title: GRCHA19_L8_mock_rep1

tag: allele

value: Mock

tag: replicate


title: MCF-7_E2-EHT SRC3_ChIPSeq rep1

description:
SRC3_ChIPSeq rep1
MCF-7_E2-EHT

value: SRC3 (Santa Cruz, sc-7216 )


title: riboseq_10uMSPD_rep2

description: Ribosome-protected RNA 17-34 nt

growth_protocol: Yeast cells grown to OD600 0.6-0.7 from starting OD 0.025 at 30 degrees in SD medium with 10 µM added SPD.

value: 10uM SPD


title: RNAseq_10uMSPD_rep1


title: RNAseq_10uMSPD_rep2


title: CLCF1_3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

data_processing:
Illumina NovaSeq 6000
An average of 33 million reads (paired-end reads of 100 bp) per sample was mapped by alignment to the human genome (GRCh38) using STAR, gene expression level was quantified using RSEM, and differentially expressed genes (DEGs) were analyzed using DESeq2 Wald test (R software packages).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited test files include count, TPM and FPKM values for each Sample

source_name: macrophage stimulated by RANKL and CLCF1

growth_protocol: Human monocytes obtained from the blood of healthy donors (Asian, 3 males with ages of 30-45 years) were isolated by density gradient centrifugation (Ficoll-PaqueTM PLUS: GE Healthcare, Waukesha, WI, USA) followed by MACS Pan monocyte isolation kit (Miltenyi Biotec, Auburn, CA, USA) 36. Cells were suspended in growth medium containing minimum essential medium Eagle (MEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), a 5% penicillin/streptomycin solution, and 5% L-glutamine and cultured in a 37°C-humidified atmosphere containing 5% CO2 in a 75 cm2 flask for 3 h. Thereafter, the medium was discarded and adherent monocytes (CD14+) were cultured in growth medium supplemented with 25 ng/ml human recombinant macrophage colony-stimulating factor (MCSF; Peprotech, Japan). After 3 days of cultivation, the adherent cells were washed 3 times with ice-cold phosphate-buffered saline (PBS; Nacalai Tesque, Kyoto, Japan) and detached by treatment with a 1% trypsin-EDTA solution (GE Healthcare). Cells were washed with PBS (Nacalai), seeded on a 96-well plate (1 x 104) and cultured in growth medium supplemented with 25 ng/ml MCSF (Peprotech, Japan) with or without 50 ng/ml of one growth factors for 8 days.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, and the integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality libraries assayed by Bioanalyzer High sensitivity DNA kit (Agilent) were subjected to Illumina NovaSeq 6000 System (Illumina).

treatment_protocol: Growth factors included human recombinant proteins of Receptor activator of nuclear factor kappa-Β ligand (RANKL),  CLCF1(R&D system) . The growth medium for the cultures was regularly replenished with fresh growth medium supplemented with each recombinant protein at 3-day intervals.

value: macrophage

value: stimulated by RANKL and CLCF1


title: MCF-7_E2-EHT SRC3_ChIPSeq rep2

description:
SRC3_ChIPSeq rep2
MCF-7_E2-EHT

value: Breast cancer cell line


title: riboseq_0SPD_rep1

description: Ribosome-protected RNA 17-34 nt


title: CLCF1_2


title: GRCHA19_L7_dex_rep1

value: 10 uM Dexamethasone


title: GRCHA19_L7_dex_rep2


title: T1D_6209


title: MCF-7_E2 SRC3_ChIPSeq rep2

description:
SRC3_ChIPSeq rep2
MCF-7_E2


title: GRCHA19_L5_mock_rep1


title: MCF-7_E2 SRC3_ChIPSeq rep1

description:
SRC3_ChIPSeq rep1
MCF-7_E2


title: riboseq_10uMSPD_rep1

description: Ribosome-protected RNA 17-34 nt


title: GRCHA19_L5_mock_rep2


title: ND_6336


title: MCF-7_EHT SRC3_ChIPSeq rep2

description:
SRC3_ChIPSeq rep2
MCF-7_EHT


title: GRCHA19_L5_dex_rep1


title: CLCF1_1


title: ND_6339


title: ND_6279


title: MCF-7_EHT SRC3_ChIPSeq rep1

description:
SRC3_ChIPSeq rep1
MCF-7_EHT


title: MCF-7_control SRC3_ChIPSeq rep2

description:
SRC3_ChIPSeq rep2
MCF-7_control


title: ND_6293


title: GRCHA19_L5_dex_rep2


title: TH_LF2

city: Jinan

first: Huawei

last: Li

address: North Industry Road

institute: Crop Research Institute, Shandong Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the pooled RNA  was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: Triticum aestivum release36_Ensembl
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Triticum aestivum

source_name: flag leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing ( 2 x 150 bp) on an Illumina Hiseq 4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

tag: developmental stage

value: grain filling stage

value: leaf

value: Take off the whole head of wheat


title: MCF-7_control SRC3_ChIPSeq rep1

description:
SRC3_ChIPSeq rep1
MCF-7_control


title: TH_LF3


title: m6A_PCIF1 KO_rep1

city: La jolla

first: Qiong

last: Zhang

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
Library strategy: m6Am-exo-seq
Fastqc was used to perform quality control on sequencing data.
cutadapt was applied to remove adapters and trim reads.
The pre-processed reads were aligned to human genome (built on Release 31 (GRCh38.p12) gencode) by STAR
MACS2(q value: 0.05, call-summit mode) was used based on its paired IP/input data.
To generate the peak distribution across chromosome region, including intron, CDS, intergenic region) and across gene region (3’UTR, 5’UTR and CDS) RSeQC and Guitar Plot were applied. The gene annotation used here is from GENCODE. For further m6Am peak analysis, we extracted common peaks whose summit is in the 5’UTR region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: m6Am genes with decreased peak density.xlsx
Supplementary_files_format_and_content: peak distribution.xls

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI containing 10% fetal bovine serum (FBS) and 50 µM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted using TRIzol. About 100mg RNA were then used to isolate poly(A) RNA using two rounds of oligo25 Dynabeads capture.
For one sample, 100 μg poly(A) RNA was fragmented in fragmenting buffer at 70°C for 15min. Fragmentation is stopped by the addition of EDTA to a final concentration of 70 mM. mRNA is purified  with the RNA Clean and Concentrator 5 kit (Zymo Research). Uncapped and fragmented transcripts are phosphorylated by treating the mRNA with 200 U of T4 PNK (NEB) in T4 ligase buffer for 1:30 h at  37°C. Then, 20 U of Terminator 5'-Phosphate-Dependent Exonuclease (Lucigen) is added with 1X Exonuclease buffer A. Samples are treated for 3 h at 30°C to remove phosphorylated (ie. uncapped and sheared) transcripts. The RNA enriched for 5'-capped transcripts is purified with the RNA clean and concentrator 5 kit (Zymo Research). 30 U of Cap-Clip (CellScript) are added and incubated for 2 h at 37°C in CAP-CLIP buffer to remove the cap. RNA is again purified with the RNA clean and Concentrator 5 kit. 10% of the treated RNA is saved as input, the rest is diluted and incubated with 5 μg of anti-m6A antibody (abcam, ab151230) at 4 °C for 2 h. 100 μl protein G magnetic beads were added to pull down the m6A immunoprecipitation complex. After wash for three times, the bound RNA was eluted in 100 μl elution buffer and purified using RNA clean and concentrator-5 kit. Final libraries amplified and were subjected to paired-end sequencing in the HT sequencing IGM Genomics core, UCSD.

treatment_protocol: 100 million control or PCIF1 KO Jurkat cells were mock treated or infected with HIV LAI strain at an MOI of 4 for 3 days.

tag: antibody

tag: cell line

value: T cell line

value: PCIF1 KO


title: ND_6232

tag: tissue

value: laser microdissected islets


title: ND_6234


title: m6A_PCIF1 KO_rep2


title: m6A_control_rep2

value: control


title: m6A_HIV_rep2

value: HIV


title: AAb_6429

value: non-diabetic islet autoantibody-positive individuals


title: ND_6131

value: control non-diabetic


title: MCF-7_EHT RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MCF-7_EHT

tag: chip antibody

value: Rac1 (Millipore, 05-389)


title: MCF-7_EHT RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF-7_EHT


title: AAb_6424


title: MCF-7_E2-EHT RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF-7_E2-EHT


title: MCF-7_E2 RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MCF-7_E2

value: 10 nM E2


title: HH_LF3

value: Take off half of the head of wheat


title: HH_LF2


title: m6A_control_rep1


title: HH_LF1


title: m6A_HIV_rep1


title: Input_HIV_rep1


title: Input_PCIF1 KO_rep2


title: MCF-7_E2-EHT RAC1_ChIPSeq rep2

description:
RAC1_ChIPSeq rep2
MCF-7_E2-EHT


title: TH_LF1


title: MCF-7_E2 RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF-7_E2


title: HH_GN3

source_name: grains

value: grains