title: Mouse_tibia_M5_ACTTGA

city: Sheffield

first: Ning

last: Wang

address: Beech Hill Road

institute: University of Sheffield

description: processed data file: Mouse_M.profiling-table.txt

data_processing:
Illumina HiSeq Control Software 2.2.38 used for basecalling
Mapping of reads to reference sequences was performed using BWA-MEM (version 0.7.10-r789)
Sequencing reads were counted on gene models with the HTSeq-count program (the –s flag set to ‘no’).
Differential gene expression was analysed with the R package edgeR v. 3.16.5.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
To obtain highly enriched populations of osteocytes, tibias of mouse were cut to expose the metaphysis and centrifuged briefly to remove bone marrow (1500g, 30 sec).  Calvarial samples were obtained from the rodents with scissors, removing the sutures and avoiding any marrow spaces (diploe). All samples were dissected free of periosteum and accessible surfaces were scraped with a scalpel. They were then immersed briefly in a 1mg/ml solution of collagenase (Sigma Aldrich) for 3-5 minutes at 37°C to remove any adherent surface cells.  Samples were then washed in saline before being snap frozen by complete submersion in liquid nitrogen and then stored at -80˚C.  Bone samples were pulverised using a mikro-dismembrator-S (Braun Biotech International GmbH Melsungen, Germany), in which the bone is shaken in a robust PTFE mill chamber with an 8mm tungsten carbide ball (both cooled in liquid nitrogen before use, and again after adding the bone pieces, before agitation).  The mill with tissue sample was placed within the mikro-dismembrator-S and set to shake at 2500rpm for 45 seconds.  The weight of the fine bone powder was recorded and it was stored for RNA extraction. 1ml of Trizol Reagent (Ambion) was added per 125mg of pulverized tissue (typical tissue amounts 350-500mg); samples were incubated in Trizol reagent for 10 minutes at room temperature.  Samples were centrifuged at 500g for 5 minutes at 4˚C, the supernatant was removed carefully to ensure no debris was transferred. 0.3ml of chloroform was added to each 1ml of Trizol reagent, the sample was thoroughly mixed and allowed to incubate at room temperature for 5 minutes.  The samples were centrifuged at 12,000g for 20 minutes at 4˚C.  The colourless upper phase was collected and transferred to a separate tube, to which an equal volume of 70% ethanol was added and incubated at room temperature for 10 minutes.    The samples were then applied to spin cartridges from TRIzol Plus RNA purification kit (Ambion) following the manufactures instructions using the optional On-Column PureLink DNase (Invitrogen) treatment step.  Samples were quantified using spectrophotometry (NanoDrop Thermo) and quality measure using a Bioanalyzer (Agilent).  Only RNA with a RNA integrity number (RIN) above 8 was stored in -80 ˚C and used for RNA-Seq. Samples used for analysis were one long bone and skull pair pooled from two rats, two long bone and skull pairs each pooled from 3 mice, and 3 long bone and skull pairs each from individual macaques.  "
cDNA library preparation and sequencing were performed by Eurofins Genomic (Ebersberg, Germany). From the total RNA sample, poly(A)+ RNA was enriched and randomized primer was used for first strand cDNA synthesis.

tag: age

value: 4 month

value: tibia

value: osteocyte


title: Mouse_tibia_M7_CGATGT

status: Public on Jul 08 2020

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: cell type


title: Mouse_calvaria_M8_GATCAG

value: calvaria


title: Mouse_calvaria_M4_ATCACG


title: CTLA4.WT.M26 [1047506]

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

country: USA

institute: Regeneron Pharmaceuticals, Inc

description:
1047506_1_1_180924_D00377_0359_BHF5W5BCX2
processed data file: b16_counts.txt

data_processing:
Array Studio software (OmicSoft) used for reads mapping.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

extract_protocol:
Total RNA was purified from all samples using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX™Turbo™DNase Buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies).
Strand-specific mRNAseq libraries were prepared from total RNA using the KAPA Stranded mRNA-Seq Kits (Kapa Biosystems).

tag: strain background

tag: genotype

value: Aire+/+

tag: treatment

value: tumor


title: Iso.WT.M22 [1047505]

description:
1047505_1_1_180924_D00377_0359_BHF5W5BCX2
processed data file: b16_counts.txt

value: Isotype control


title: CTLA4.KO.M16 [1047501]

description:
1047501_1_1_180924_D00377_0359_BHF5W5BCX2
processed data file: b16_counts.txt

value: Aire-/-


title: Iso.WT.M19 [1047503]

description:
1047503_1_1_180924_D00377_0359_BHF5W5BCX2
processed data file: b16_counts.txt


title: Iso.KO.M14 [1047499]

description:
1047499_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: Iso.KO.M15 [1047500]

description:
1047500_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: Iso.KO.M13 [1047498]

description:
1047498_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: CTLA4.KO.M12 [1047497]

description:
1047497_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: CTLA4.KO.M11 [1047496]

description:
1047496_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: CTLA4.KO.M10 [1047495]

description:
1047495_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: CTLA4.KO.M8 [1047494]

description:
1047494_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: M5_WT_tumor [993286]

description:
993286_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M4_KO_tumor [993285]

description:
993285_1_1_171103_SN7001209_0743_ACBKCVACXX_L4
processed data file: mc38_counts.txt


title: M6_WT_spleen [993280]

description:
993280_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt

source_name: spleen

value: spleen


title: M7_WT_spleen [993281]

description:
993281_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M3_KO_tumor [993284]

description:
993284_1_1_171103_SN7001209_0743_ACBKCVACXX_L4
processed data file: mc38_counts.txt


title: Iso.KO.M1 [1047489]

description:
1047489_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: Iso.KO.M2 [1047490]

description:
1047490_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: M6_WT_tumor [993287]

description:
993287_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: CTLA4.KO.M5 [1047491]

description:
1047491_1_1_180924_D00377_0358_AHF5YCBCX2
processed data file: b16_counts.txt


title: M8_WT_spleen [993282]

description:
993282_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M5_WT_spleen [993279]

description:
993279_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M8_WT_tumor [993289]

description:
993289_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M4_KO_spleen [993278]

description:
993278_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M3_KO_spleen [993277]

description:
993277_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M8_WT_ln [993274]

description:
993274_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt

source_name: lymph node

value: lymph node


title: M1_KO_spleen [993275]

description:
993275_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M2_KO_spleen [993276]

description:
993276_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: Iso.WT.M21 [1047504]

description:
1047504_1_1_180924_D00377_0359_BHF5W5BCX2
processed data file: b16_counts.txt


title: M4_KO_ln [993270]

description:
993270_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M7_WT_ln [993273]

description:
993273_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M6_WT_ln [993272]

description:
993272_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M5_WT_ln [993271]

description:
993271_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M3_KO_ln [993269]

description:
993269_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M2_KO_ln [993268]

description:
993268_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: M1_KO_tumor [993283]

description:
993283_1_1_171103_SN7001209_0743_ACBKCVACXX_L4
processed data file: mc38_counts.txt


title: M7_WT_tumor [993288]

description:
993288_1_1_171103_SN7001209_0743_ACBKCVACXX_L6
processed data file: mc38_counts.txt


title: M1_KO_ln [993267]

description:
993267_1_1_171103_SN7001209_0743_ACBKCVACXX_L5
processed data file: mc38_counts.txt


title: H3K9/14Ac_DKO3_200114

city: Fukuoka

first: SHINYA

last: TANAKA

address: 3-1-1, maidashi, Higashi-ku

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
Quality check and adaprtor triming were performed using TrimGalore version 0.6.4 with the following setting: -q 30 --length 35
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version 1.2.2) with the following setting: -n 3 -m 1 -a --best --strata
Peaks were identified using macs2 (version 2.1.2) with setting minimum QVALUE cutoff = 0.01.
Genome_build: mm10

molecule: genomic DNA

source_name: B cells

extract_protocol:
Soluble chromatin was prepared from sonicated nuclei and the sobule chromatin was immunoprecipitated with antibodies.
Libraries were prepared with NEBnext Ultra II DNA library prep kit or ThruPLEX DNA-Seq Kit.

value: Primary B cells

value: Freshly isolated from spleen

tag: chip antibody

value: Acetylated H3 (Merck Millipore, 06-599)


title: H3K9/14Ac_CTL1_200114


title: H3K9/14Ac_DKO2_190729


title: H3K9/14Ac_DKO1_190729


title: HDAC2_DKO2

value: HDAC2 (GeneTex, GTX109642)


title: HDAC2_CTL3


title: HDAC2_CTL1


title: HDAC1_DKO2

value: HDAC1 (GeneTex, GTX100513)


title: HDAC2_CTL2


title: HDAC1_DKO1


title: HDAC1_CTL1


title: Liver, T+_dox_EtOH (rep 4)

city: Philadelphia

first: Gary

middle: D

last: Wu

state: PA

address: 915 Biomedical Research Building, 421 Curie Blvd

department: Department of Medicine, Division of Gastroenterology

institute: University of Pennsylvania

data_processing:
raw data (*.fastq.gz) was aligned to the transcriptome using salmon, and summarized to gene level with tximport
Genome_build: GRCm38.p6, Gencode version M19 for gene models
Supplementary_files_format_and_content: non normalized transcript counts summarized to gene level - comma separated values

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Invitrogen Purelink RNA Isolation Kit.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) as per standard protocol

value: ASAH+

tag: induction

value: no

tag: diet

value: 28% ethanol-derived calories, 4 weeks

value: Liver


title: Liver, T+_dox_EtOH (rep 3)


title: HDAC2_DKO1


title: Liver, T+_dox_EtOH (rep 1)


title: Liver, T+_dox_EtOH (rep 2)


title: Liver, T+_noInd_EtOH (rep 5)

value: yes


title: HDAC1_CTL2


title: Liver, T+_noInd_EtOH (rep 4)


title: Liver, t-_dox_EtOH (rep 4)

value: ASAH-


title: Liver, t-_dox_EtOH (rep 3)


title: Liver, T+_noInd_EtOH (rep 2)


title: Liver, t-_dox_EtOH (rep 2)


title: Input_CTL2

data_processing:
Quality check and adaprtor triming were performed using TrimGalore version 0.6.4 with the following setting: -q 30 --length 35
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version 1.2.2) with the following setting: -n 3 -m 1 -a --best --strata
Peaks were identified using macs2 (version 2.1.2) with setting minimum QVALUE cutoff = 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and HDAC1 or HDAC2 complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBnext Ultra II DNA library prep kit.

value: wild type


title: Liver, t-_dox_EtOH (rep 1)


title: Input_CTL1


title: H3K9/14Ac_CTL1_190729


title: FNcKO 48 hr PCS rep 1

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

description: FNcKO 48 hr PCS rep1

data_processing:
Analysis was performed by the University of Delaware Bioinformatics Core Facility using a modified MAPRseq pipeline implemented on the BioMix compute cluster at the Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute
Sequence quality was assessed using FASTQC
Sequences were end-trimmed (Q30) and filtered (no ambiguous nucleotides, 35bp minimum length after trimming) using Trim Galore (v0.4.4)
Trimmed reads were aligned to the reference genome using Tophat v2.1.0
Mapping quality was assessed using RSeQC v2.3.7 and metrics extracted from BedTools v2.17 and SamTools v1.4
Feature counts were extracted using HtSeq v0.6.1p1
Pairwise differential expression analysis was performed on features with >1 cpm in at least 2 samples using EdgeR v 3.16.5
Genome_build: Mus musculus mm10 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: "Chr" (Chromosome), "GeneID" (Gene Symbol),  GeneCount (Read Count), RPKM

source_name: Lens

extract_protocol:
By using an in vivo mouse model of cataract surgery, fiber cells were removed from wild type (WT) and Fibronectin conditional knockout (FNcKO) lenses via a central corneal incision, leaving behind the lens capsule and attached LECs. Samples were harvested at 0 hour and 48 hours PCS, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for Stradeded TruSeq Library Preparation Kit for the Illumina HiSeq 2500

value: Mixed (C57BL/6, 129, FVB/N)

value: Lens capsule and attached LECs

value: Adult 2 month old

value: Fibronectin conditional knockout

tag: time point


title: FNcKO 0 hr PCS rep 3

description: FNcKO 0 hr PCS rep3


title: FNcKO 48 hr PCS rep 3

description: FNcKO 48 hr PCS rep3


title: FNcKO 0 hr PCS rep 1

description: FNcKO 0 hr PCS rep1


title: WT 48 hr PCS rep 3

description: WT 48 hr PCS rep3


title: WT 48 hr PCS rep 1

description: WT 48 hr PCS rep1


title: WT 48 hr PCS rep 2

description: WT 48 hr PCS rep2


title: WT 0 hr PCS rep 1

description: WT 0 hr PCS rep1


title: KO brown fat 3

city: Cambridge

first: Nai-Jia

last: Huang

state: MA

address: 455 Main Street

institute: Whitehead Institute

data_processing:
single-end sequencing (50 cycles).   Sequences were aligned to mouse genome (mm9) using STAR (version 2.5.4b) with Ensembl  gene model version 67. After reads were checked for strandness with infer_experiment.py function from RSeQC , only reverse stranded reads were assigned to genes with STAR.
Genome_build: mm9
Supplementary_files_format_and_content: gene counts in text

source_name: KO brown fat

extract_protocol:
Mature brown fat is isolated from minced adipose tissues which were digested with collagenase A. The mature adipocytes was obtaibed in the upper lipids layer after centrifugation at 700 g for 5 min. RNA were extracted using QIazol reagent and RNAeasy kit (Qiagen.)
mRNA library was prepared using KAPA Hyper mRNA kit

value: 6 weeks old

tag: genotype/variation

value: PHOSPHO1 knockout (KO)

value: mature brown fat


title: KO brown fat 2


title: WT 0 hr PCS rep 3

description: WT 0 hr PCS rep3


title: WT brown fat 2

source_name: WT brown fat


title: WT brown fat 3


title: WT brown fat 1


title: KO brown fat 1


title: Liver, T+_noInd_EtOH (rep 3)


title: Liver, T+_noInd_EtOH (rep 1)


title: FNcKO 48 hr PCS rep 2

description: FNcKO 48 hr PCS rep2


title: FNcKO 0 hr PCS rep 2

description: FNcKO 0 hr PCS rep2


title: WT 0 hr PCS rep 2

description: WT 0 hr PCS rep2


title: 1130_Asc_24hr Rep 2

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from MCF-7, ascorbic acid, 24 hour

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

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

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

organism: Homo sapiens

source_name: MCF-7, ascorbic acid, 24 hour, rep 2

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

growth_protocol: MCF-7 breast tumor cells were grown in RPMI 1640 media containing 10% FBS.

extract_protocol: RNA was extracted using Triazol method.

treatment_protocol: Cell were left untreated or treated with ascorbic acid , topotecan or combinations of ascorbic acid and topotecan for 1 hr and 24 hr.

tag: cells

tag: gender

value: Female


title: 1130_Asc_24hr Rep 3

source_name: MCF-7, ascorbic acid, 24 hour, rep 3


title: 1130_Asc_Top_24hr Rep 3

description: Gene expression from MCF-7, ascorbic acid + topotecan, 24 hour

source_name: MCF-7, ascorbic acid + topotecan, 24 hour, rep 3


title: 1130_Control_24hr Rep 3

description: Gene expression from MCF-7, control, 24 hour

source_name: MCF-7, control, 24 hour, rep 3


title: 1130_Top_24hr Rep 2

description: Gene expression from MCF-7, topotecan, 24 hour

source_name: MCF-7, topotecan, 24 hour, rep 2


title: 1130_Asc_Top_24hr Rep 2

source_name: MCF-7, ascorbic acid + topotecan, 24 hour, rep 2


title: 1130_Asc_Top_24hr Rep 1

source_name: MCF-7, ascorbic acid + topotecan, 24 hour, rep 1


title: 1130_Asc_Top Rep 3

description: Gene expression from MCF-7, ascorbic acid + topotecan, 0 hour

source_name: MCF-7, ascorbic acid + topotecan, 0 hour, rep 3


title: 1130_Top_24hr Rep 3

source_name: MCF-7, topotecan, 24 hour, rep 3


title: 1130_Asc_24hr Rep 1

source_name: MCF-7, ascorbic acid, 24 hour, rep 1


title: 1130_Top Rep 2

description: Gene expression from MCF-7, topotecan, 0 hour

source_name: MCF-7, topotecan, 0 hour, rep 2


title: 1130_Asc_Top Rep 1

source_name: MCF-7, ascorbic acid + topotecan, 0 hour, rep 1


title: 1130_Top_24hr Rep 1

source_name: MCF-7, topotecan, 24 hour, rep 1


title: U251_E2F2_E2F8_KO_E2F8_2

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

description:
E2F2_E2F8_counts.tsv
U251_E2F8_2

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v0.4.3)
The trimmed Ribo-seq reads were aligned to the human reference genome sequence (Ensembl GRCh38.p7) using STAR aligner (v.2.5.2b) with  GENCODE v25 as a guided reference annotation, allowing a mismatch of at most two positions  --outFilterMismatchNmax 2. For RNA-seq STARlong was used allowing a total of 100 mismatches (--outFilterMismatchNmax 100) and aminimum match of 66% (--outFilterMatchNminOverLread 0.66)
Read abundance files were generated using featurecounts
Genome_build: hg38
Supplementary_files_format_and_content: raw counts table

molecule: polyA RNA

source_name: brain/CNS

growth_protocol: U251 and U343 control and MSI1 KO cells were plated in 96 wells at a density of 8x104. Cells were synchronized by serum starvation for 24 hours. Following synchronization, cells were exposed to 20 nM of Paclitaxel for 24 hours. Cells were fixed in 4% PFA and stained with Alpha-Tubulin and DAPI. The experiment was performed in triplicates and 1,000 cells were counted per replicate. Differences were assessed with a student’s t-test. p < 0.01.

extract_protocol:
After 24 hours the cells were treated with the different inhibitors or DMSO. Plates were transferred to the IncuCyte automated microscope system (Essen BioScience) and cells were counted every 2 hours for 5–7 days.
RNA-seq samples were prepared according to Illumina protocols and sequenced at UTHSCSA Genome Sequencing Facility.

tag: cell line

value: glial

value: reverse

tag: disease

value: Glioblastoma,ud

value: Grade IV

tag: ethinicity

value: caucasian


title: U251_E2F2_E2F8_KO_E2F8_3

description:
E2F2_E2F8_counts.tsv
U251_E2F8_3


title: U251_E2F2_E2F8_KO_E2F8_1

description:
E2F2_E2F8_counts.tsv
U251_E2F8_1


title: 1130_Top Rep 1

source_name: MCF-7, topotecan, 0 hour, rep 1


title: 1130_Asc Rep 1

description: Gene expression from MCF-7, ascorbic acid, 0 hour

source_name: MCF-7, ascorbic acid, 0 hour, rep 1


title: 1130_Top Rep 3

source_name: MCF-7, topotecan, 0 hour, rep 3


title: 1130_Asc Rep3

source_name: MCF-7, ascorbic acid, 0 hour, rep 3


title: 1130_Asc_Top Rep 2

source_name: MCF-7, ascorbic acid + topotecan, 0 hour, rep 2


title: 1130_Control Rep 3

description: Gene expression from MCF-7, control, 0 hour

source_name: MCF-7, control, 0 hour, rep 3


title: 1130_Control Rep 1

source_name: MCF-7, control, 0 hour, rep 1


title: 1130_Control_24hr Rep 2

source_name: MCF-7, control, 24 hour, rep 2


title: 1130_Asc Rep2

source_name: MCF-7, ascorbic acid, 0 hour, rep 2


title: U251_E2F2_E2F8_KO_E2F2_2

description:
E2F2_E2F8_counts.tsv
U251_E2F2_2


title: U251_E2F2_E2F8_KO_E2F2_3

description:
E2F2_E2F8_counts.tsv
U251_E2F2_3


title: pqm-1  CoCl2 (20hr) vs N2 CoCl2 (20hr), repl. 3

city: Freiburg

first: Thomas

last: Heimbucher

state: Baden Württemberg

address: Schaenzlestrasse 1

department: Biologie III

country: Germany

institute: Thomas Heimbucher

description: N2 and pqm-1(ok485) comparison + CoCl2, 20hr induced, repl.3

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 5 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 12.0.2.2
Datafile type : Agilent result file

organism: Caenorhabditis elegans

source_name: N2 CoCl2

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

extract_protocol: Extraction method : Qiagen Rneasy Kit

treatment_protocol:
Compound Based Treatment : 5 mM CoCl2
Time : 20 hr

tag: strain name

source_name: pqm-1 CoCl2

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

treatment_protocol:
Time : 20 hr
Compound Based Treatment : 5 mM CoCl2


title: 1130_Control_24hr Rep 1

source_name: MCF-7, control, 24 hour, rep 1


title: pqm-1  CoCl2 (20hr) vs N2 CoCl2 (20hr), repl. 1

description: N2 and pqm-1(ok485) comparison + CoCl2, 20hr induced, repl.1


title: U251_E2F2_E2F8_KO_Control_3

description:
E2F2_E2F8_counts.tsv
U251_Control_3

value: Control


title: U251_E2F2_E2F8_KO_Control_1

description:
E2F2_E2F8_counts.tsv
U251_Control_1


title: U251_E2F2_E2F8_KO_Control_2

description:
E2F2_E2F8_counts.tsv
U251_Control_2


title: U343_MSI1_KO_Control_2

description:
U343_counts.tsv
U343WT_2_S16

value: WT


title: U343_MSI1_KO_Control_1

description:
U343_counts.tsv
U343WT_1_S15


title: U343_MSI1_KO_Control_3

description:
U343_counts.tsv
U343WT_3_S17


title: U343_MSI1_KO_Clone4_3

description:
U343_counts.tsv
U343Msi1CRISPR_cl4_3_S23


title: 1130_Control Rep 2

source_name: MCF-7, control, 0 hour, rep 2


title: pqm-1  CoCl2 (20hr) vs N2 CoCl2 (20hr), repl. 2

description: N2 and pqm-1(ok485) comparison + CoCl2, 20hr induced, repl.2


title: U343_MSI1_KO_Clone4_2

description:
U343_counts.tsv
U343Msi1CRISPR_cl4_2_S22


title: U343_MSI1_KO_Clone4_1

description:
U343_counts.tsv
U343Msi1CRISPR_cl4_1_S21


title: U343_MSI1_KO_Clone1_2

description:
U343_counts.tsv
U343Msi1CRISPR_cl1_2_S19


title: U343_MSI1_KO_Clone1_3

description:
U343_counts.tsv
U343Msi1CRISPR_cl1_3_S20


title: pqm-1 control (20hr) vs N2 control, repl. 2

description: N2 and pqm-1(ok485) comparison, 20 hr control, repl.2

source_name: N2 control

treatment_protocol:
Compound Based Treatment : 0 mM CoCl2
Time : 20 hr

source_name: pqm-1(ok485) control

treatment_protocol:
Time : 20 hr
Compound Based Treatment : 0 mM CoCl2


title: N2 CoCl2 (20hr) vs N2 control, repl. 3

description: N2 CoCl2 exposure 20hr repl. 3

source_name: N2 - CoCl2

source_name: N2 + CoCl2


title: pqm-1 CoCl2 (20hr) vs pqm-1 control, repl. 1

source_name: pqm-1 control


title: pqm-1 control (20hr) vs N2 control, repl. 3

description: N2 and pqm-1(ok485) comparison, 20 hr control, repl.3


title: N2 CoCl2 (20hr) vs N2 control, repl. 2

description: N2 - and + CoCl2 replicate 2


title: pqm-1  CoCl2 (6hr) vs N2 CoCl2 (6hr), repl. 3

description: N2 and pqm-1(ok485) comparison, 6hr CoCl, repl.3

treatment_protocol:
Compound Based Treatment : 5 mM CoCl2
Time : 6 hr

treatment_protocol:
Time : 6 hr
Compound Based Treatment : 5 mM CoCl2


title: pqm-1  CoCl2 (6hr) vs N2 CoCl2 (6hr), repl. 2

description: N2 and pqm-1(ok485) comparison, 6hr CoCl, repl.2


title: pqm-1 control (20hr) vs N2 control, repl. 1

description: N2 and pqm-1(ok485) comparison control, repl.1


title: U343_MSI1_KO_Clone1_1

description:
U343_counts.tsv
U343Msi1CRISPR_cl1_1_S18

source_name: brain/CNS


title: U251_MSI1_KO_Control_3

description:
U251_counts.tsv
Control_3_S12

value: unstranded


title: U251_MSI1_KO_Control_2

description:
U251_counts.tsv
Control_2_S11


title: U251_MSI1_KO_Control_1

description:
U251_counts.tsv
Control_1_S10


title: U251_MSI1_KO_Clone5_3

description:
U251_counts.tsv
Clone_5_3_S18

value: Clone


title: N2 CoCl2 (20hr) vs N2 control, repl. 1b

description: N2 CoCl2 exposure 20hr repl. 1b

value: wild type


title: U251_MSI1_KO_Clone3_3

description:
U251_counts.tsv
Clone_3_3_S15


title: U251_MSI1_KO_Clone5_1

description:
U251_counts.tsv
Clone_5_1_S16


title: U251_MSI1_KO_Clone3_2

description:
U251_counts.tsv
Clone_3_2_S14


title: U251_MSI1_KO_Clone3_1

description:
U251_counts.tsv
Clone_3_1_S13


title: pqm-1 control (6hr) vs N2 control, repl. 2

description: N2 and pqm-1(ok485) comparison control, 6hr, repl.2

source_name: N2 contol

treatment_protocol:
Compound Based Treatment : 0 mM CoCl2
Time : 6 hr

source_name: pqm-1 contol

treatment_protocol:
Time : 6 hr
Compound Based Treatment : 0 mM CoCl2


title: pqm-1 control (6hr) vs N2 control, repl. 3

description: N2 and pqm-1(ok485) comparison control, 6hr, repl.3


title: pqm-1 CoCl2 (20hr) vs pqm-1 control, repl. 2


title: pqm-1 control (6hr) vs N2 control, repl. 1b

description: N2 and pqm-1(ok485) comparison control, 6hr, repl.1b


title: pqm-1  CoCl2 (6hr) vs N2 CoCl2 (6hr), repl. 1

description: N2 and pqm-1(ok485) comparison, 6hr CoCl2, repl.1

source_name: pqm1 CoCl2


title: pqm-1 CoCl2 (6hr) vs pqm-1 control, repl. 3

description: Pqm-1 CoCl2 exposure 6hr repl. 3

source_name: Pqm-1 control

source_name: Pqm-1 CoCl2


title: BRD3 RIP-seq  H1 hESC differentiated to definitive endoderm for 4 days rep 2

city: Boston

first: Alan

middle: C.

last: Mullen

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
The RIP-seq 150bp paired-end reads were trimmed using Trimgalore
STAR(v2.7.3a) was used to map the trimmed reads to the human genome
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Deeptools genomeCoverage tool (Count per million normalized RNA-seq read converage track)

source_name: H1 human Embryonic stem cells (hESC)

growth_protocol: H1 (WA01) cells (WiCell) were cultured in mTeSR1 (Stem Cell Technologies) in feeder-free conditions as described (Daneshvar et al, 2016).

extract_protocol:
Each RNA immunoprecipitation (RIP) reaction was performed on 12 million nuclei. Nuclei of cells were isolated by suspending the cells in a hypotonic buffer (20 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) for 15 minutes, adding NP-40 to a final concentration of 0.5% and then centrifuging for 10 minutes at 850 g. Nuclei were then lysed in RIP buffer (150 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5 mM DTT, 0.5% NP-40, RNase-inhibitor, and protease inhibitor). Nuclear membranes and debris were pelleted by centrifugation at 16,000 g for 10 minutes. 5 μg of each antibody (BRD3 antibody: Bethyl Laboratories, catalog number: A302-368A, Normal Rabbit IgG: Cell Signaling Technology, catalog number: 2729) was added to each lysate and incubated in a rotator at 4˚C for 3 hours. 40 μL of protein G Dynabeads (Thermo Fisher) was added to each reaction and incubated for one hour on a rotator at 4˚C. Beads were precipitated on a magnetic rack and washed three times with RIP buffer and one time in DPBS. Beads were resuspended in Trizol, and RNA was extracted for library preparation.
RIP-seq libraries were prepared according to instructions accompanying the Ultralow RNA Library Prep Kit for Illumina.

treatment_protocol: hESCs were differentiated for 4 days in RPMI with B27 supplement in the presence of 50 ng/ml activin A (R&D Systems) as previously described (Daneshvar et al., 2016)

value: hESC cells

tag: state

value: Differentiated in RPMI, B27 supplement, and 50 ng/mL activin

tag: rip antibody

value: BRD3 (Bethyl Laboratories, catalog number:A302-368A)

tag: fraction

value: BRD3-bound Immunoprecipitated RNA


title: IgG RIP-seq  H1 hESC differentiated to definitive endoderm for 4 days

tag: cell type

value: Normal Rabbit IgG (Cell Signaling Technology, catalog number:2729)

value: IgG-bound Immunoprecipitated RNA


title: pqm-1 CoCl2 (20hr) vs pqm-1 control, repl. 3

description: pqm-1 CoCl2 exposure 20hr repl. 3

source_name: pqm-1 - CoCl2

tag: genotype

source_name: pqm-1 + CoCl2


title: BRD3 RIP-seq  H1 hESC differentiated to definitive endoderm for 4 days rep 1


title: pqm-1 CoCl2 (6hr) vs pqm-1 control, repl. 1b

description: pqm1 CoCl2 exposure 6hr repl. 1b

source_name: pqm1 control


title: pqm-1 CoCl2 (6hr) vs pqm-1 control, repl. 2

description: Pqm-1 CoCl2 exposure 6hr repl. 2

source_name: N2 CoCl2


title: N2 CoCl2 (6hr) vs N2 control, repl. 2

description: N2 CoCl2 exposure 6hr repl. 2


title: genomic DNA from umbilical cord 15

type: genomic

city: Salt, Girona

first: Anna

last: Prats-Puig

state: Girona

address: Francesc Macia 65

country: Spain

institute: EUSES. Escola Universitària de la Salut i l'Esport.

hyb_protocol: bisulphite converted DNA was analyzed using Infinium MethylationEPIC Kit using standard protocol

scan_protocol: not provided

data_processing: Minify R-package (version 1.26.2)

label: Cy5, Cy3

source_name: Umbilical cord tissue 15

label_protocol: Infinium MethylationEPIC Kit

extract_protocol: Genomic DNA was extracted from the Wharton’s jelly and blood vessels using the Gentra PureGene tissue kit (Qiagen). Sodium bisulfite conversion of DNA was performed, and the chemically modified DNA was then used to analyze the methylation status of over 850,000 individual CpGs in umbilical cord tissue using the Infinium Methylation EPIC Bead Chip microarray (Illumina) at IIS La Fe (Valencia, Spain).

value: Female

tag: tissue

value: Umbilical cord

tag: disease state

value: gestational obesity


title: genomic DNA from umbilical cord 16

source_name: Umbilical cord tissue 16


title: input RNA-seq H1 hESC differentiated to definitive endoderm for 4 days

value: total RNA


title: BRD3 RIP-seq  H1 hESC rep 2

value: Cultured in mTESR1


title: N2 CoCl2 (6hr) vs N2 control, repl. 3

description: N2 CoCl2 exposure 6hr repl. 3

source_name: N2 control


title: BRD3 RIP-seq  H1 hESC rep 1


title: input RNA-seq H1 hESC


title: IgG RIP-seq  H1 hESC


title: BM stem cell-derived OSCC-2

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: 7.5 µg fragmented and labeled cRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlasTM imaging station.

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

label: Biotin

source_name: Oral mucosa

label_protocol: 500 ng of total RNA was labeled using a GeneChipTM 3' IVT PLUS Reagent Kit (Affymetrix) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted by lysing the tissues with Isogen (Nippon Gene) after homogenization with a TissueLyser (Qiagen) according to the manufacturer's instructions.

value: Oral squamous cell carcinoma


title: genomic DNA from umbilical cord 13

source_name: Umbilical cord tissue 13

value: normal


title: BM stem cell-derived OSCC-1-2


title: RP2-R120X.rep1

city: London

first: Michael

middle: E

last: Cheetham

address: 11-43 Bath Street

institute: University College London

data_processing:
Raw .fastq sequences were cleaned from any residual sequencing adapter using  cutadapt with parameters -m 20 and -e 0.1
Fragments were aligned to the human genome  (build 38, Ensembl version 92) using STAR.
Genes were quantified in each sample by using featurecounts and summarised in a single tab-delimited text file.
Genome_build: hg38 ( Ensembl version 92)
Supplementary_files_format_and_content: tab-delimited text file containing a matrix of raw counts-per-gene values for all samples.

source_name: RP2-R120X.retinal organoid

extract_protocol:
Retinal organoids or half retinal organoids were subjected to RNA extraction using RNeasy  MicroKit (Qiagen) following homogenization with 19, 21 and 30 gauge needle and sent for sequencing to Otogenetics (Atlanta - GA, US).
RNA libraries were prepared for sequencing using standard reverse stranded Illumina protocols

tag: developmental stage

value: 150-days old

tag: tissue/cell type

value: retinal organoid


title: N2 CoCl2 (6hr) vs N2 control, repl. 1

description: N2 CoCl2 exposure 6hr repl. 1


title: genomic DNA from umbilical cord 14

source_name: Umbilical cord tissue 14


title: Uterine stromal cells isolated from Hif1 cKO mice on day 5 of pregnancy

city: Urbana

first: Indrani

middle: C

last: Bagchi

state: IL

address: 2001 S Lincoln

department: Comparative Biosciences

institute: Univ of Illinois at Urbana Champaign

description: D5 cKO sample

hyb_protocol: 10 micrograms of labeled cRNA were hybridized to a Mouse Genome 430A 2.0 Affymetrix 3' Expression Analysis Array.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_2.

source_name: Mouse uterine stromal cells

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Hif1 floxed mice  were crossed with PRcre mice to conditionally ablate Rac1 in the uterus.

extract_protocol: Trizol extraction of total RNA was performed followed by RNA cleaup using the Rneasy (Qiagen) according to the manufacturer's instructions

treatment_protocol: Hif2-null mice (n=3) and the corresponding controls (n=3) were mated to fertile male mice. The presence of vaginal plug after mating was designated as day 1 of pregnancy. On day 5 of pregnancy, uterine horns were excised and submitted to enzymatic digestion to isolate teh stromal cells.

value: Hif2 alpha-null

tag: time point

value: on day 5 of pregnancy

value: uterine stromal cells


title: RP2-KO.rep1

source_name: RP2-KO.retinal organoid

value: BJ CRISPR/Cas9 KO for RP2


title: RP2-R120X.rep3


title: genomic DNA from umbilical cord 11

source_name: Umbilical cord tissue 11


title: genomic DNA from umbilical cord 12

source_name: Umbilical cord tissue 12


title: Uterine stromal cells isolated from Hif1 flox control mice on day 5 of pregnancy

description: D5 Flox Sample

tag: genotype/variation

value: Hif2 alpha-intact


title: Normal OSCC-13


title: U251_MSI1_KO_Clone5_2

description:
U251_counts.tsv
Clone_5_2_S17

source_name: brain/CNS

value: glial

value: Clone

value: unstranded

value: Glioblastoma,ud

value: Grade IV

value: caucasian


title: Normal OSCC-11


title: Normal OSCC-12


title: Control.rep3

source_name: Control.retinal organoid

value: BJ


title: Control.rep2


title: Control.rep1


title: genomic DNA from umbilical cord 10

source_name: Umbilical cord tissue 10

value: Female

value: Umbilical cord

value: gestational obesity


title: RP2-R120X.rep2

value: 150-days old


title: genomic DNA from umbilical cord 9

source_name: Umbilical cord tissue 9

value: normal


title: Normal OSCC-10

value: Oral squamous cell carcinoma


title: RP2-KO.rep2

value: retinal organoid


title: genomic DNA from umbilical cord 8

source_name: Umbilical cord tissue 8


title: 0524-2_4_75_batch5

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

data_processing:
Paired end reads were mapped using STAR to hg38 with Gencode v25 annotations.
Gene expression levels were quantified using rsem (v1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts

source_name: human cortical spheroids

growth_protocol: hiPSC were grown as in Yoon et al., 2019, Nature Methods.

extract_protocol:
Following extraction of total RNA, rRNA was depleted (RiboZero Gold, Illumina) and libraries were prepared using Truseq stranded RNA RiboZero Gold (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: F

tag: iPSc line

value: Control

tag: differntiation

tag: differentiation day

tag: batch


title: 1208-2_7_75_batch5


title: Normal OSCC-8


title: Normal OSCC-9


title: 1208-2_4_75_batch5


title: 0294-1_4_75_batch5


title: genomic DNA from umbilical cord 7

source_name: Umbilical cord tissue 7

tag: gender


title: 8119-2_4_100_batch5

value: M


title: Normal OSCC-7


title: 0524-1_4_50_batch5


title: 8119-2_4_75_batch5


title: genomic DNA from umbilical cord 6

source_name: Umbilical cord tissue 6


title: 0524-1_5_75_batch5


title: 8119-2_7_50_batch5


title: Normal OSCC-6


title: 0524-1_4_25_batch5


title: 8119-1_6_50_batch5


title: 1208-2_7_100_batch5


title: 0524-2_4_100_batch5


title: BM stem cell-derived OSCC-1-1


title: genomic DNA from umbilical cord 5

source_name: Umbilical cord tissue 5


title: U251_E2F2_E2F8_KO_E2F2_1

description:
E2F2_E2F8_counts.tsv
U251_E2F2_1

tag: cell line

value: glial

value: reverse

tag: disease

tag: ethinicity


title: Normal OSCC-4

source_name: Oral mucosa


title: 8119-1_6_25_batch5


title: genomic DNA from umbilical cord 3

source_name: Umbilical cord tissue 3


title: 1208-2_5_100_batch5


title: 8119-2_6_25_batch5


title: 8119-2_6_100_batch5


title: 8119-2_7_25_batch5


title: Normal OSCC-5


title: genomic DNA from umbilical cord 1

source_name: Umbilical cord tissue 1


title: Normal OSCC-3


title: Normal OSCC-2


title: 0307-1_4_50_batch5


title: genomic DNA from umbilical cord 2

source_name: Umbilical cord tissue 2


title: BMDM_WT_24h_1

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: femurs and tibias

growth_protocol: Bone marrow cells were flushed from femurs and tibias of male mice between 6 and 9 weeks of age, and were grown in DMEM/F12 (Thermo Fisher) supplemented with 10% FBS (HyClone), 1% penicillin–streptomycin (Thermo Fisher), 1% l-glutamine (Thermo Fisher), and 40 ng/ml of recombinant mouse M-CSF (576406; BioLegend) for 7-8 days. The medium was changed every 3 days. Differentiated BMDMs were detached from plates using StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) and replated into 12-well tissue culture dishes at a density of 5 x 105 cells per well prior to cell stimulation.

extract_protocol: Poly-A mRNA was extracted from total RNA by using an Oligo-dT beads of NEBNext Poly(A) RNA Magneic Isolation Module (NEB), after which RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.

tag: time

tag: strain

tag: cell type

value: bone marrow-derived macrophage

value: wild-type

value: male


title: BMDM_WT_24h_2

tag: genotype


title: BMDM_WT_24h_3


title: 0524-2_4_50_batch5


title: 1208-2_4_50_batch5


title: 1208-2_4_25_batch5


title: BMDM_WT_12h_3


title: BMDM_WT_12h_2


title: 0524-1_5_25_batch5


title: 8119-2_7_100_batch5


title: 1208-2_5_25_batch5


title: 8119-1_6_100_batch5


title: 1208-2_5_75_batch5


title: BMDM_WT_8h_3


title: BMDM_WT_12h_1


title: 0307-1_4_25_batch5


title: 8119-2_6_50_batch5


title: Normal OSCC-1

tag: tissue


title: 0524-2_4_25_batch5


title: genomic DNA from umbilical cord 4

source_name: Umbilical cord tissue 4

tag: disease state


title: 8119-1_4_50_batch5


title: BMDM_WT_8h_1


title: 0294-1_4_50_batch5


title: 8119-2_7_75_batch5


title: Rat_tibia_R3_TAGCTT

description: processed data file: Rat_R.profiling-table.txt

data_processing:
Illumina HiSeq Control Software 2.2.38 used for basecalling
Mapping of reads to reference sequences was performed using BWA-MEM (version 0.7.10-r789)
Sequencing reads were counted on gene models with the HTSeq-count program (the –s flag set to ‘no’).
Differential gene expression was analysed with the R package edgeR v. 3.16.5.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

extract_protocol:
To obtain highly enriched populations of osteocytes, tibias of rat were cut to expose the metaphysis and centrifuged briefly to remove bone marrow (1500g, 30 sec).  Calvarial samples were obtained from the rodents with scissors, removing the sutures and avoiding any marrow spaces (diploe). All samples were dissected free of periosteum and accessible surfaces were scraped with a scalpel. They were then immersed briefly in a 1mg/ml solution of collagenase (Sigma Aldrich) for 3-5 minutes at 37°C to remove any adherent surface cells.  Samples were then washed in saline before being snap frozen by complete submersion in liquid nitrogen and then stored at -80˚C.  Bone samples were pulverised using a mikro-dismembrator-S (Braun Biotech International GmbH Melsungen, Germany), in which the bone is shaken in a robust PTFE mill chamber with an 8mm tungsten carbide ball (both cooled in liquid nitrogen before use, and again after adding the bone pieces, before agitation).  The mill with tissue sample was placed within the mikro-dismembrator-S and set to shake at 2500rpm for 45 seconds.  The weight of the fine bone powder was recorded and it was stored for RNA extraction. 1ml of Trizol Reagent (Ambion) was added per 125mg of pulverized tissue (typical tissue amounts 350-500mg); samples were incubated in Trizol reagent for 10 minutes at room temperature.  Samples were centrifuged at 500g for 5 minutes at 4˚C, the supernatant was removed carefully to ensure no debris was transferred. 0.3ml of chloroform was added to each 1ml of Trizol reagent, the sample was thoroughly mixed and allowed to incubate at room temperature for 5 minutes.  The samples were centrifuged at 12,000g for 20 minutes at 4˚C.  The colourless upper phase was collected and transferred to a separate tube, to which an equal volume of 70% ethanol was added and incubated at room temperature for 10 minutes.    The samples were then applied to spin cartridges from TRIzol Plus RNA purification kit (Ambion) following the manufactures instructions using the optional On-Column PureLink DNase (Invitrogen) treatment step.  Samples were quantified using spectrophotometry (NanoDrop Thermo) and quality measure using a Bioanalyzer (Agilent).  Only RNA with a RNA integrity number (RIN) above 8 was stored in -80 ˚C and used for RNA-Seq. Samples used for analysis were one long bone and skull pair pooled from two rats, two long bone and skull pairs each pooled from 3 mice, and 3 long bone and skull pairs each from individual macaques.  "
cDNA library preparation and sequencing were performed by Eurofins Genomic (Ebersberg, Germany). From the total RNA sample, poly(A)+ RNA was enriched and randomized primer was used for first strand cDNA synthesis.

value: Wistar

tag: age

value: 6 month

value: tibia

value: osteocyte


title: 1208-2_7_25_batch5


title: BMDM_WT_4h_3


title: Rat_calvaria_R1_TGACCA

value: calvaria


title: 0294-1_4_25_batch5


title: BMDM_WT_4h_2


title: BMDM_WT_8h_2


title: Fish26

city: Bodø

first: Pål

middle: A.

last: Olsvik

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
The library preparations were sequenced on an Illumina 2000 platform and 50 bp single-end reads were generated. Clean reads were obtained by removing reads containing adapter, reads containing poly-N (>10%) and low-quality reads (if the percentage of the low-quality base (base with quality value ≤ 5) is greater than 50% in a read) from raw data.
Alignment and mapping were conducted by using SOAPaligner/SOAP2 (Li et al., 2009) and the in house made Salmo salar lens transcriptome (allowing no more than 2 bases mismatch in the alignment). About 74% of clean reads (17,882,297±823,801, n=26, mean±SEM) mapped to transcriptome contigs. The number of clean reads for each gene was calculated and normalized to Reads Per Kb per Million of reads (RPKM). Deep analysis was performed based on DEGs, including Gene Ontology (GO), KEGG pathway enrichment analysis, and protein-protein interaction networks.
Genome_build: In-house transcriptome made from RNA extracted from 10 diploid lenses and 10 triploid lenses.
Supplementary_files_format_and_content: Excel file with each line consisting of Salmo salar sequence name (Gene ID), and raw counts for all 26 samples. KEGG orthologs, GO, and Blast nr hits are provided in the Excel file.

organism: Salmo salar

source_name: Lens

extract_protocol:
Lens tissue was thoroughly homogenized before RNA extraction using a Precellys 24 homogenizer and ceramic beads CK28 (Bertin Technologies, Montigny-le-Bretonneux, France). Total RNA was extracted using the BioRobot EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany), treated with DNase. The RNA integrity number (RIN) of RNA extracted for RNA-seq (2N: n=12, 3N: n=14) was 8.2±0.1 (n=26) (mean ± SEM). according to the manufacturer's instructions and eluted in 50 μL RNase-free MilliQ H2O.
Poly (A) mRNA was isolated using magnetic beads with oligo (dT) from total RNA obtained from the lens samples. Fragmentation buffer was added to shred mRNA to short reads. Using these short fragments (about 200 bp) as templates, random hexamer primers were applied to synthesize first-strand cDNA. Second-strand cDNA was synthesized using buffer, dNTPs, RNaseH, and DNA polymerase I. QiaQuick PCR extraction kit (Qiagen) was used to purify short double-stranded cDNA fragments according to manufacturer’s instructions. These fragments were then resolved with EB buffer for end reparation, added poly (A), and ligated to the sequencing adapters. After agarose gel electrophoresis, the suitable fragments were selected for PCR amplification as templates.

treatment_protocol: No specific treatment except sorting fish according to ploidy.

value: Lens

tag: group

value: Triploid with cataract

tag: FISH body weight (g)

tag: FISH length (cm)


title: 1208-2_4_100_batch5

tag: Sex

tag: iPSc line

tag: differntiation


title: BMDM_WT_4h_1

tag: gender


title: 1208-2_7_50_batch5

tag: differentiation day

tag: batch


title: Fish25


title: 0307-1_4_100_batch5


title: 0524-1_5_100_batch5


title: 8119-1_4_100_batch5


title: 0294-1_4_100_batch5


title: Fish24


title: BMDM_WT_0h_3


title: BMDM_WT_0h_2


title: 8119-2_6_75_batch5


title: Fish23


title: 0524-1_4_100_batch5


title: 0524-1_5_50_batch5


title: Fish22


title: BMDM_KO_24h_3

value: lncFAO knockout


title: 0307-1_4_75_batch5


title: Fish21


title: 8119-2_4_50_batch5


title: BMDM_WT_0h_1


title: 0524-1_4_75_batch5


title: 1208-2_5_50_batch5


title: BMDM_KO_24h_2


title: 8119-1_6_75_batch5


title: Fish20


title: PFA8_L DNAm

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: R package ChAMP v2.14.0

label: Cy5 and Cy3

source_name: PFA_tumor-derived line

label_protocol: Standard Illumina Protocol

growth_protocol: All Posterior fossa ependymoma tissues were dissociated as quickly as possible upon receiving from OR. Tissues were minced small and dissociated as single cells with Collagenase/dispase (Roche) and incubated at 37C for 30 minutes with gentle vortex every 10 minutes. After 30 minutes incubation, cells were passed through 70um cell strainer and pelleted by centrifugation. Pellets were dissolved in EPN cell culture media and seeded (1*10^6 cells/per plate) on to   precoated laminin Primaria plates (Corning) with EPN cell culture media. Cells were replenished with fresh EPN cell culture media every 3 days. All the PFA cell cultures implicated in the study were established and maintained as continuous culture at 1% Hypoxia.

extract_protocol: DNA was extracted from snap frozen tumour tissue and frozen cell pellets using the Qiagen AllPrep Universal kit and eluted into EB.

tag: sample type

value: tumour-derived line

tag: tumour type

value: Posterior fossa type A (PFA) ependymomas

value: 4 years


title: 2242-1_8_50_batch4

value: M

value: Control


title: BMDM_KO_24h_1

tag: time

tag: strain


title: PFA5_T DNAm

value: tumour sample

value: Unknown


title: Fish19


title: 8119-2_4_25_batch5


title: 8119-1_4_25_batch5


title: 2242-1_8_25_batch4


title: 2242-1_8_75_batch4


title: BMDM_KO_12h_3

tag: cell type

value: bone marrow-derived macrophage

tag: genotype


title: PFA5_L DNAm


title: 6803-3_17_75_batch3_redo


title: 2242-1_8_100_batch4


title: Fish18

tag: tissue

value: Triploid without cataract


title: BMDM_KO_12h_2

value: male


title: PFA4_T DNAm

value: F

tag: age

value: 2 years


title: 8826-3_17_75_batch3_redo


title: Fish17

tag: group


title: BMDM_KO_12h_1


title: 1658-2_17_75_batch3_redo


title: PFA2_T DNAm

value: 9 months


title: PFA1_T DNAm

value: 3 years


title: PFA8_T DNAm


title: Fish16

value: Lens

tag: FISH body weight (g)


title: 7946-5_17_75_batch3_redo


title: 7946-3_17_75_batch3_redo


title: 2637-3_17_75_batch3_redo


title: Fish15

tag: FISH length (cm)


title: BMDM_KO_8h_2


title: Fish14


title: BMDM_KO_8h_1


title: 0524-2_12_75_batch3_redo

tag: Sex


title: Fish13


title: BMDM_KO_4h_3


title: Fish12

value: Diploid with cataract


title: 0904-4_15_75_batch3_redo

tag: iPSc line


title: 0524-1_12_75_batch3_redo

tag: differntiation


title: BMDM_KO_8h_3

value: lncFAO knockout

tag: gender


title: 9050-3_16_75_batch3_redo

tag: differentiation day


title: 6803-3_17_50_batch3

tag: batch


title: 6803-3_17_100_batch3


title: BMDM_KO_4h_2


title: 6803-3_17_75_batch3


title: Fish11


title: 2723-1_11_75_batch3_redo


title: 6803-3_17_25_batch3


title: PFA1_L DNAm

tag: sample type

value: tumour-derived line


title: Fish9


title: Fish10


title: BMDM_KO_4h_1


title: BMDM_KO_0h_3


title: PFA2_L DNAm

tag: tumour type

value: Posterior fossa type A (PFA) ependymomas


title: 8826-3_17_50_batch3


title: BMDM_KO_0h_2

tag: time


title: 8826-3_17_75_batch3


title: 8826-3_17_100_batch3


title: 8826-3_17_25_batch3


title: Fish8


title: 1658-2_17_100_batch3


title: PFA4_L DNAm


title: BMDM_KO_0h_1

tag: strain


title: Tet KO CD93-CD23-CD21 Io B cells-3 (S13216)

data_processing:
Read alignment: Bowtie2 v2.1.0  and TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
FPKM (Fragments per Kirobase per Million reads) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: CSV files containing FPKM values

source_name: B cells

extract_protocol:
Total RNA was isolated using RNeasy micro kit (Qiagen)
DNA library preparation for RNA-Seq analysis using a SureSelect Strand-Specific RNA Library Prep Kit for Illumina Multiplexed Sequencing (Agilent Technologies).

tag: cell type

value: Primary B cells

value: Freshly isolated from spleen

tag: cell markers

value: CD93-CD23-CD21 Io


title: Fish6

tag: tissue

value: Diploid without cataract


title: Fish5


title: 1658-2_17_75_batch3


title: Tet KO CD93-CD23-CD21 Io B cells-1 (S13214)

tag: genotype


title: 1658-2_17_25_batch3


title: 1658-2_17_50_batch3


title: 7946-5_17_100_batch3


title: Tet KO CD93-CD23+CD21 Int B cells-3 (S13210)

value: CD93-CD23+CD21 Int


title: 7946-5_17_75_batch3


title: 7946-5_17_25_batch3


title: 7946-5_17_50_batch3


title: 7946-3_17_100_batch3


title: Tet KO CD93-CD23+CD21 Int B cells-2 (S13205)


title: 7946-3_17_75_batch3


title: 7946-3_17_25_batch3


title: 7946-3_17_50_batch3


title: Fish3

tag: group


title: Tet KO CD93-CD23+CD21 Int B cells-1 (S13200)


title: Fish2

tag: FISH body weight (g)


title: 2637-3_17_100_batch3

value: M


title: 2637-3_17_75_batch3


title: Fish1

tag: FISH length (cm)


title: Fish7


title: Tet KO CD93-CD23-CD21 Io B cells-2 (S13215)


title: Tet KO CD93+ B cells-3 (S13222)


title: Fish4


title: CC053d5_3

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC, then trimmed using Trimgalore with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner with default settings.
Mapped reads were feature counted (per gene) using RsubRead. Raw counts from mouse genome and virus mapping were then combined, an offset of 1 was added and counts were then normalized using DESeq2. After normalization, single extreme outlier points were razorized.
Log2 transformed, normalized expression levels were then batch corrected using package sva.
Extreme outlier samples were identified in principle component analyses and removed. For each group, 3-4 replicates were retained. Log2 transformed, normalized and batch corrected expression levels were then used for further analyses.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
For tissue preparation, mice were sacrificed and entire lungs were extracted. Lungs were immediately transferred to RNAlater solution, kept at 4°C for one day and subsequently stored at -20°C. RNA was isolated using Qiagen Midi Kit as described previously. RNA quality was controlled on a 2100 Bioanalyzer Instrument (Agilent).
500ng of total RNA was used to prepare libraries for sequencing using the Lexogen SENSE mRNA-seq library kit for Ion Torrent. Libraries amplified for 11 cycles as the final step of library preparation. Before sequencing, 1ul aliquots of this material was pooled and sequenced on an Ion Torrent PGM 314 chip. Barcode quantification data from the PGM were used to balance the barcodes for final pooling before sequencing. Following this final pooling, the library pools were sized to a target size of 260bp on a Pippin Prep instrument using the 2% Pippin Agarose gel. The sized libraries were examined on an Agilent High Sensitivity DNA chip, quantified using real-time PCR, and used to prepare spheres using a One-Touch 2 device.
RNA-Seq; These spheres were then sequenced on an Ion Torrent Proton sequencer with a P1 chip. The mean number of reads per sample was 24 million.

treatment_protocol: Female, 8-12 weeks old mice were anesthetized by intra-peritoneal injection with Ketamine/Xylazine. Mice were then intra-nasally infected with 20µl virus solution (10 ffu) and body weight, survival and well-being of mice was monitored for the following 14 days.

tag: agent

value: mouse-adapted H3N2 virus

tag: day

tag: ffu

tag: Sex

value: female

tag: strains


title: 2637-3_17_25_batch3

tag: iPSc line

tag: differntiation

tag: differentiation day

tag: batch


title: CC053d5_2


title: 9050-7_16_100_batch3

value: F


title: Tet KO CD93+ B cells-2 (S13221)

city: Fukuoka

first: SHINYA

last: TANAKA

address: 3-1-1, maidashi, Higashi-ku

institute: Kyushu University

tag: strain


title: 9050-7_16_75_batch3


title: 9050-3_16_100_batch3


title: Tet KO CD93+ B cells-1 (S13220)

tag: cell type


title: 9050-3_16_75_batch3


title: CC053d5_1


title: CC053d3_5


title: CTL CD93-CD23-CD21 Io B cells-2 (S13212)

value: control

tag: cell markers


title: 1728-7_9_100_batch3


title: CTL CD93-CD23-CD21 Io B cells-3 (S13213)

tag: tissue


title: 9050-3_16_25_batch3


title: 1728-7_9_75_batch3


title: CC053d3_4


title: CTL CD93-CD23-CD21 Io B cells-1 (S13211)

tag: genotype


title: CC053d3_2


title: 6032-4_16_50_batch3

value: Control


title: 6032-4_16_25_batch3


title: CTL CD93-CD23+CD21 Int B cells-3 (S13198)


title: 2637-3_17_50_batch3


title: 0904-4_15_100_batch3


title: CC053d3_1


title: CTL CD93-CD23+CD21 Int B cells-2 (S13197)


title: 0904-4_15_75_batch3


title: CC053cd3_3

value: ctrl


title: 0904-4_15_50_batch3


title: 9050-3_16_50_batch3


title: CTL CD93-CD23+CD21 Int B cells-1 (S13196)


title: 0904-4_15_25_batch3


title: CC053cd3_2


title: 0524-2_14_100_batch3


title: CC053cd3_1


title: 0524-2_14_75_batch3


title: CTL CD93+ B cells-2 (S13218)


title: 0524-2_14_50_batch3


title: 1728-7_9_50_batch3


title: 0524-2_12_100_batch3


title: 0524-2_12_75_batch3


title: CTL CD93+ B cells-1 (S13217)


title: 0524-2_12_50_batch3


title: CC051d5_4


title: CC051d5_5


title: Tet DKO CD93- B cells-3 (S15080)


title: Tet DKO CD93- B cells-2 (S15079)


title: 0524-1_13_75_batch3


title: 0524-1_13_100_batch3


title: 0524-2_12_25_batch3


title: CC051d5_2


title: 0524-1_13_50_batch3


title: Tet DKO CD93- B cells-1 (S15077)


title: 0524-1_13_25_batch3


title: CC051d3_3


title: 0524-1_12_100_batch3


title: CTL CD93+ B cells-3 (S13219)


title: 0524-2_14_25_batch3


title: 0524-1_12_75_batch3


title: CTL CD93- B cells-3 (S15076)


title: CC051d3_2


title: 0524-1_12_50_batch3


title: CTL CD93- B cells-2 (S15074)


title: 0524-1_12_25_batch3


title: 2723-1_11_100_batch3


title: CTL CD93- B cells-1 (S15072)


title: 2723-1_11_75_batch3


title: CC051cd3_3


title: CC051d5_3


title: CC051d3_1


title: 2723-1_11_25_batch3


title: 7958-3_12_75_batch2


title: KO3_rep3

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Adaptors were trimmed from the 3' ends of sequenced reads with cutadapt (-O 1 -m 15).
Alignment was performed by Salmon v0.14.1 (-l ISR --numBootstraps 1000 --seqBias --gcBias --validateMappings --mimicBT2) using the selective alignment procedure utilising a decoy-aware transcriptome index built from the GRCm38 reference sequence and customised GENCODE vM21 gene annotation.
Differential gene expression analysis was performed with DESeq2 v1.24.0 and tximport v1.12.3, using apeglm v1.6.0 for log2 fold change shrinkage.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 normalized gene counts for all samples in .txt format, plus DESeq2 differential expression results for each KO (1/2/3) vs WT comparison in .txt format.

source_name: NIH-3T3 cell culture

growth_protocol: NIH-3T3 cells were cultured at 37˚C in humidified 95% air/5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Life Technologies) containing: glucose (4.5 g/L), glutamine (2 mM), foetal bovine serum (10%), penicillin (100 U/ml), streptomycin sulphate (100 μg/ml), sodium pyruvate (1 mM), and uridine (50 μg/ml).

extract_protocol:
RNA was isolated from NIH-3T3 cells using an miRNeasy MiniKit (Qiagen), incorporating an on-column RNase-free DNA digestion, according to the manufacturer’s instructions.
Total RNA libraries were prepared according to the Illumina TruSeq protocol, using random hexamer primers for cDNA generation and the Ribo-Zero rRNA removal kit for cytoplasmic RNA deptetion.

treatment_protocol: NIH-3T3 cells were seeded in 6-well plates at 60% confluency, allowed to attach, and transfected with 1.5 μg of a pD1311-AD mammalian Cas9 expression vector (ATUM) encoding a Crls1-targeting gRNA using FuGENE HD (Promega) in Opti-MEM (Invitrogen, Thermofisher). For establishing stably transfected colonies, single-cell sorting was performed on the transfected cell population 72 hours post-transfection; where individual cells were sorted into 96-well plates based on GFP fluorescence signal using a FACSAria II in PBS + 2%FBS (v/v) (BD Biosciences). Loss of Crls1 alleles was confirmed by both Sanger sequencing and Nextera sequencing of PCR amplified gDNA performed by the Australian Genomic Research Facility (AGRF).

tag: cell line


title: 7958-3_12_25_batch2


title: CC051cd3_2


title: 7958-3_12_50_batch2


title: KO3_rep2


title: CC051cd3_1


title: 6303-5_12_100_batch2


title: CC041d5_5


title: KO3_rep1


title: KO2_rep3


title: CC041d5_4


title: 6303-5_12_75_batch2


title: 6303-5_12_50_batch2


title: KO2_rep2


title: 6303-4_12_100_batch2


title: CC041d5_3


title: 6303-4_12_75_batch2


title: 6303-4_12_50_batch2


title: KO2_rep1


title: 7958-3_12_100_batch2


title: 6303-4_12_25_batch2


title: 9050-7_16_75_batch3_redo


title: CC041d5_2


title: 1804-5_10_100_batch2


title: KO1_rep3


title: 1804-5_10_75_batch2


title: 1804-5_10_50_batch2


title: KO1_rep2


title: CC041d3_4


title: 1804-5_9_100_batch2


title: 1804-5_9_75_batch2


title: CC041d3_3


title: CC041d3_6


title: 1804-5_9_25_batch2


title: WT_rep3


title: 1804-5_9_50_batch2


title: WT_rep2


title: 1728-7_3_100_batch2


title: CC041d3_2


title: CC041cd3_3


title: KO1_rep1


title: 1728-7_3_50_batch2


title: WT_rep1


title: 1728-7_3_25_batch2


title: sc_Tak1_HEP_Ripk1D138N_D138N

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

country: China

institute: IRCBC

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to rat with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis. And for sc-seq comparison, Sequencing reads were mapped to dme with cellranger count by default parameter. The count files were used as input to Seurat for downstream analysis.
Genome_build: mm19
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue. And Seurat was used for single cell downstream analysis

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa) and single cell isolated by cell strainer (Falcon, 352340)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01) and sc-seq libraries were prepared according to instructions of 10X single cell  library  kit v3 (Chromiun, 1000078).

tag: strain background

tag: age

value: 6 weeks

value: Liver


title: CC041cd3_1


title: CYN-iPSC-MSC-P5B-FP-001

city: Hawthorn North

first: Kilian

last: Kelly

state: Victoria

address: PO Box 7165

institute: Cynata Therapeutics Limited

data_processing:
Sequencing reads were adapter and quality trimmed using the Skewer trimming program (v0.1.123)
Quality reads were subsequently aligned to the annotated reference genome using the STAR aligner (v2.5.0a\n)
Quantification of expression for each gene was calculated by RSEM (v1.2.26)
The expected read counts from RSEM were filtered for low/empty values and used for differential gene expression analysis using EdgeR (v3.12.1)
RSEM uses input transcriptome alignment by STAR and estimate expression values using the alignments. Expression levels are quantified through FPKM (Fragments Per Kilobase of  transcript per Million mapped reads), TPM, and read counts.
Genome_build: GRCh37p13
Supplementary_files_format_and_content: Excel file, showing Fragment per kilobase of exon per million reads mapped (FPKM), Transcripts Per Million (TPM), and read counts of genes and transcripts inferred by RSEM.

source_name: CD34-enriched peripheral blood mononuclear cells

growth_protocol: MSCs were seeded as single cells at 1.3x10^4 cells/cm2 in mesenchymal serum free expansion medium on fibronectin/collagen 1 coated plasticware and incubated at 37°C, 5% CO2, 20% O2 (normoxic) for ~3 days per passage

extract_protocol:
Total RNA was extracted from iPSC-derived MSC samples, from which mRNA was then isolated.
Prepared using standard Illumina protocols

value: iPSC-derived mesenchymal stromal cells

tag: passage level


title: 0537-3_2_100_batch2


title: 1804-5_10_25_batch2


title: CP3 Norm

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
RNA-seq aligned to hg19 genome and UCSC refrence transcript with STAR(version 2.4.0).
Bedgraph file generated from bedGraph generted by bedtoolsbedtools then normalized to the same scale by regenrating a normalized bigwig.
New bigwig files are converted to bigwig format by bedGraphToBigWig .
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Peripheral blood progenitor cells

growth_protocol: CD34+ hematopoietic cells were isolated from blood using a ficoll gradient to isolate mononuclear cells. This was followed by the selection of CD34+ cells via magnetic column.

extract_protocol:
Suspension cells were harvested by centrifugation. RNA was extracted with the Qiagen RNeasy mRNA kits following manufacturer's instructions
Only RNA with RIN>7 was used. Library prep was performed using the illumina Truseq Stranded Total RNA kit with Ribozero Gold. Sequencing depth of 200M reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD34+ cells were cultured in Stempro media and human cytokine mix for 96h prior to harvesting for RNA

tag: origin

value: Chronic phase CML patient peripheral blood

value: CD34+ Hematopoietic progenitor cells


title: sc_Tak1f_f_Ripk1D138N_D138N_rep3


title: CC036d5_4

tag: agent

tag: day

tag: ffu


title: CP2 Norm


title: 0537-3_2_75_batch2

source_name: human cortical spheroids

tag: Sex

tag: iPSc line


title: CC036d5_2

tag: strains


title: CP1 Norm


title: sc_Tak1f_f_Ripk1D138N_D138N_rep2


title: 0537-3_2_50_batch2

tag: differntiation

tag: differentiation day

tag: batch


title: 0537-3_2_25_batch2


title: CC036d5_1


title: 0804-1_2_100_batch2


title: CYN-iPSC-MSC-P5B-FP-003

tag: cell type


title: CYN-iPSC-MSC-P5B-FP-002


title: CC036d3_3


title: sc_Tak1f_f_rep2

tag: tissue


title: BM4 Norm

source_name: Bone marrow dreived progenitor cells

value: Normal bone marrow


title: CC041cd3_2


title: BM3 Norm


title: CC036d3_2


title: 0804-1_2_75_batch2


title: 0804-1_2_50_batch2


title: w12_Tak1_HEP_Ripk1D138N_D138N_rep4

value: 12 weeks

tag: genotype


title: CC036cd3_3


title: CC036d3_1


title: sc_Tak1f_f_rep1


title: sc_Tak1_HEP


title: 0804-1_2_25_batch2


title: w12_Tak1_HEP_Ripk1D138N_D138N_rep3


title: SRSF1_IM_rep3

data_processing:
RNA-seq aligned to hg19 genome and UCSC refrence transcript with STAR(version 2.4.0).
Bigwig files are converted by bedGraphToBigWig from bedGraph generted by bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: ATCC

growth_protocol: K562 cells were obtained commercially from ATCC and maintained in RPMI supplemented with 10% FBS and 1% pen-strep. Cells were transduced with virus packaging either the SRSF1 gene or an empty vector control

extract_protocol:
Suspension cells were harvested by centrifugation. RNA was extracted with the Qiagen RNeasy mRNA kits following manufacturer's instructions
Only RNA with RIN>7 was used. Library prep was performed using the illumina Truseq Stranded Total RNA kit with Ribozero Gold. Each experimental condition for RNA-seq was performed in triplicate, each at a sequencing depth of 50M reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transduced cells were treated for 48 h with 0.5uM imatinib

value: Human-derived blast crisis CML cell line

tag: cell line


title: CC036cd3_2


title: 0307-1_1_100_batch2


title: sc_Tak1f_f_Ripk1D138N_D138N_rep1

tag: strain background


title: CC036cd3_1


title: 0307-1_1_75_batch2


title: SRSF1_IM_rep2


title: SRSF1_IM_rep1


title: BM2 Norm


title: w12_Tak1_HEP_rep4

tag: age


title: CC019d5_2


title: 0307-1_1_50_batch2


title: w12_Tak1_HEP_Ripk1D138N_D138N_rep1


title: w12_Tak1_HEP_rep3


title: SRSF1_DMSO_rep2


title: SRSF1_DMSO_rep3


title: 1205-4_1_100_batch2


title: BM1 Norm


title: w12_Tak1_HEP_rep2


title: CC019d5_1


title: SRSF1_DMSO_rep1


title: w12_Tak1_HEP_rep1


title: CC019d3_5


title: CC019d3_4


title: vector_IM_rep3


title: w12_Tak1_HEP_Ripk1D138N_D138N_rep2


title: 1205-4_1_50_batch2


title: CC019d3_3


title: CC019d5_3


title: w12_Tak1f_f_Ripk1D138N_D138N_rep3


title: 1205-4_1_25_batch2


title: vector_IM_rep1


title: CC019d3_2


title: 0307-1_1_25_batch2


title: w12_Tak1f_f_Ripk1D138N_D138N_rep2


title: 0410-1_1_75_batch2


title: vector_DMSO_rep3


title: CC019cd3_3


title: w12_Tak1f_f_Ripk1D138N_D138N_rep1


title: 1205-4_1_75_batch2


title: CC019cd3_2


title: vector_DMSO_rep1


title: 0410-1_1_50_batch2


title: vector_DMSO_rep2


title: CC019cd3_1


title: 0410-1_1_25_batch2


title: vector_IM_rep2


title: CC006d5_4


title: w12_Tak1f_f_Ripk1D138N_D138N_rep4


title: w12_Tak1f_f_rep2


title: 8858-3_1_100_batch2


title: Resident fibroblast transfected with stealth AURKB siRNA, rep2

city: Cincinnati

first: Anil

middle: G

last: Jegga

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Lung resident fibroblasts

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: TGFalpha mice

value: Lung resident fibroblasts

tag: treatment

value: AURKB siRNA


title: Resident fibroblast transfected with stealth AURKB siRNA, rep3


title: w12_Tak1f_f_rep3


title: 8858-3_1_75_batch2

value: M


title: w12_Tak1f_f_rep1


title: Resident fibroblast transfected with stealth AURKB siRNA, rep1


title: CC006d5_1

tag: agent

value: mouse-adapted H3N2 virus

value: female


title: 8858-3_1_50_batch2


title: w12_Tak1f_f_rep4


title: Resident fibroblast transfected with stealth control siRNA, rep3

value: control siRNA


title: w6_Tak1_HEP_Ripk1D138N_D138N_rep4


title: CC006d3_4

tag: day


title: 8858-3_1_25_batch2

value: Control


title: Resident fibroblast transfected with stealth control siRNA, rep2


title: CC006d3_3

tag: ffu


title: w6_Tak1_HEP_Ripk1D138N_D138N_rep2


title: w6_Tak1_HEP_Ripk1D138N_D138N_rep3


title: Resident fibroblast transfected with stealth control siRNA, rep1


title: CC006d5_2

tag: Sex


title: 2242-1_10_75_batch2

tag: iPSc line


title: CC006d3_2

tag: strains


title: w6_Tak1_HEP_Ripk1D138N_D138N_rep1


title: 2242-1_10_100_batch2

tag: differntiation


title: CC006d3_1


title: w6_Tak1_HEP_rep4


title: 2242-1_10_50_batch2

tag: differentiation day


title: CC006cd3_3

value: ctrl


title: w6_Tak1_HEP_rep3

value: 6 weeks


title: CC006cd3_2


title: 2242-1_10_25_batch2

tag: batch


title: 0410-1_1_100_batch2

value: F


title: w6_Tak1_HEP_rep2

value: Liver


title: RNA-seq_TT-2

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: UNAM

data_processing:
After filtering, clean reads are mapped to reference using BWA / Bowtie2  tool
Genes expression level is quantified by a software package called RSEM
The file all.gene. FPKM.txt is a expression table for all samples with brief gene description and annotation.
Then they used the alignment result to calling peak (MACS (Model-based Analysis for ChIP -seq, version: MACS-1.4.2)
We used HOMER for the differential analysis
Supplementary_files_format_and_content: bigwig, peak, FPKM

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell tratment wiht DMSO or TPL for 4 h

tag: cell type

value: Breast


title: CC006cd3_1


title: RNA-seq_TT-1


title: PQ_9h_126uM_rep1

city: Hillsboro

first: Brendan

last: Stamper

state: OR

department: Pharmacy

institute: Pacific University

description: TAMH cells treated with 126uM paraquat for 9 h (replicate 1)

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: Gene array strips were scanned using the Affymetrix GeneAtlas System at the Pacific University School of Phrmacy Research Laboratory.

data_processing: Affymetrix Expression Console v1.1 RMA normalization log2

label: biotin

label_protocol: RNA was processed for hybridization to Affymetrix Mouse Gene 2.1 ST array strips according to the manufacturer’s instructions.

growth_protocol: TAMH cells were grown in Dulbecco's Modified Eagle Medium/Ham's F-12 (1:1) media supplemented with 100nm dexamethasone, 10nM nicotinamide, 0.1% (v/v) gentamicin, and an ITS premix containing insulin (5mg/mL), transferrin (5mg/mL) and selenium (5ng/mL).  Cell passages between 30 and 40 were grown in a humidified incubator with 5% CO2 and 95% air at 37C.  During passages, cells were incubated for approximately one minute with trypsin.  Cell detachment was monitored using a microscope.  Once detachment was complete, 5mL of 0.5mg/mL soybean trypsin inhibitor in Hank’s balanced salt solution was added before plating.

extract_protocol: RNA was isolated from TAMH cells dosed with 18uM DQ, 126uM PQ or control culture media at the 9-hour timepoints.  For each treatment, cells were grown to confluence in three 150cm2 tissue culture dishes and dosed.  At the end of each treatment, cells were harvested using a rubber scraper.  Cell pellets were collected by centrifugation, and washed using ice-cold DPBS.  Trizol reagent was added to the DPBS-washed pellet, vortexed and passed through a 22G needle multiple times to ensure complete cell lysis.  Chloroform was then added, and the mixture was spun in a microcentrifuge at 8200g.  The aqueous phase was isolated and dissolved in 70% ethanol.  The resulting mixture was loaded onto a Qiagen RNeasy column.  Purified total RNAs were eluted in sterile water according to the manufacturer’s protocol.

treatment_protocol: Cell treatments consisted of exposure to either media alone or toxicologically relevant concentrations of diquat (18uM) or paraquat (126uM) for 9 h.

value: TAMH


title: CC005d5_3


title: w6_Tak1_HEP_rep1

tag: tissue


title: RNA-seq_T-2

value: DMSO


title: w6_Tak1f_f_Ripk1D138N_D138N_rep4

tag: genotype


title: PQ_9h_126uM_rep2

tag: cell line


title: w6_Tak1f_f_Ripk1D138N_D138N_rep3

tag: strain background


title: RNA-seq_T-1


title: DQ_9h_18uM_rep3

description: TAMH cells treated with 18uM diquat for 9 h (replicate 1)


title: CC005d5_1


title: CC005d5_2


title: CC005d3_3


title: RNA-seq_NTT-2


title: w6_Tak1f_f_Ripk1D138N_D138N_rep1

tag: age


title: CC005d3_2


title: DQ_9h_18uM_rep1


title: PQ_9h_126uM_rep3


title: w6_Tak1f_f_rep4


title: CC005d3_1


title: CON_9h_rep2

description: TAMH cells treated with media alone (control) for 9 h (replicate 2)


title: CON_9h_rep1

description: TAMH cells treated with media alone (control) for 9 h (replicate 1)


title: CON_9h_rep3

description: TAMH cells treated with media alone (control) for 9 h (replicate 3)


title: RNA-seq_NT-1


title: DE_BRD3IP_rep2: BRD3 ChIP-seq H1 hESC differentiated to definitive endoderm for 4 days

city: Boston

first: Alan

last: Mullen

address: 55 Fruit St.

institute: Massachusetts General Hospital

description: The signal tracks of BRD3 ChIP of hESC differentiated at 4 hr after subtracting the background (WCE) (generated by MACS2)

data_processing:
ChIP-seq data were mapped o human reference genome (hg38) by bowtie2. The mapped reads were processed using MACS2 to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: Mapped ChIP-seq reads were processed with MACS2.

source_name: BRD3 H1 human Embryonic stem cells (hESC)

extract_protocol:
BRD3 ChIP was pefromed using an anti-BRD3 (Bethyl A302-368A)
ChIP-seq libraries were prepared according to instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina.

value: H1 human Embryonic stem cells (hESC)

tag: state

value: Differentiated in RPMI, B27 supplement, and 50 ng/mL activin


title: w6_Tak1f_f_rep3


title: DE_BRD3IP_rep1: BRD3 ChIP-seq H1 hESC differentiated to definitive endoderm for 4 days


title: w6_Tak1f_f_Ripk1D138N_D138N_rep2


title: w6_Tak1f_f_rep2


title: CC005cd3_1


title: CC005cd3_2


title: DQ_9h_18uM_rep2


title: H1_BRD3IP_rep2: BRD3 ChIP-seq H1 hESC

description: The signal tracks of BRD3 ChIP of hESC differentiated at 0 hr after subtracting the background (WCE) (generated by MACS2)

value: Cultured in mTESR1


title: RNA-seq_NTT-1


title: CC004d5_3


title: CC004d5_2


title: H1_BRD3IP_rep1: BRD3 ChIP-seq H1 hESC


title: DE_input: ChIP-seq WCE H1 hESC differentiated to definitive endoderm for 4 days

source_name: WCE  H1 human Embryonic stem cells (hESC)


title: w4_Tak1_HEP_Ripk1D138N_D138N_rep4

value: 4 weeks


title: w4_Tak1_HEP_Ripk1D138N_D138N_rep3


title: CC004d3_3


title: CC004d5_1


title: w4_Tak1_HEP_Ripk1D138N_D138N_rep1


title: RNA-seq_NT-2


title: H1_input: ChIP-seq WCE H1 hESC

data_processing:
ChIP-seq data were mapped to the human reference genome (hg38) by bowtie2. The mapped reads were processed using MACS2 to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: Mapped ChIP-seq reads were processed with MACS2.


title: w4_Tak1_HEP_rep4


title: w4_Tak1_HEP_rep3


title: CC005cd3_3


title: CC004d3_2


title: w4_Tak1_HEP_rep2


title: CC004cd3_3


title: w4_Tak1_HEP_rep1


title: Sample 145_WT.3L

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
Reads with an average quality score below 25 (from any 10-bp window) or a mismatched barcode were removed
Paired-end reads were then merged using the software FLASH
Merged reads were analyzed using the QIIME pipeline with default parameters to remove chimeric, pick 97%-identity OTUs and assign taxonomy
Genome_build: Greengenes 13_8
Supplementary_files_format_and_content: csv: Includes OTUs and abundances that were detected in the dataset as well as taxonomic lineages for OTUs

source_name: WT_EAE_62_fecal pellet

growth_protocol: The mice were maintained on a 12 hours light/dark cycle with lights on at 7am. Animals were housed 2–3 per cage and cages were randomly assigned to control or experimental groups.

extract_protocol:
Whole genomic DNA was isolated via phenol-chloroform extraction. Briefly, a fecal pellet was placed in a 2 mL tube containing 200 μL silica-zirconia beads (0.1 mm). The tube was filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution.
For 16S rRNA sequencing, the V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide. Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform.

treatment_protocol: Chronic stress was started after at least 1 week of acclimation. All behavioral interventions were performed between 4 pm and 7 pm and take-downs were performed between 11am and 2 pm. Animals were excluded from the experiments if they developed illnesses (e.g. dermatitis) that might affect the outcome of the results. Mice were subjected daily to an acute stressor (1–2 hours: restraint, loud white noise, crowded housing, strobe light) and an overnight stressor (12–24 hours: 45° cage tilting, repeated cage changes, wet bedding, dark deprivation) presented in a randomized fashion. For restraint stress, mice were placed in clean 50 mL conical tubes with pierced holes for ventilation for 1 hour. For crowded housing stress, mice were placed on top of the cage wire for 2 hours, after which their cage was changed. For wet bedding stress, 200 mL of water was added to the bedding of a clean cage. All procedures used autoclaved, sterile materials (bedding, water) in order to prevent contamination.

value: 8 weeks

value: WT

tag: treatment

value: EAE

tag: experiment day

tag: sample type

value: fecal pellet


title: w4_Tak1f_f_Ripk1D138N_D138N_rep4


title: w4_Tak1f_f_Ripk1D138N_D138N_rep3


title: CC004cd3_1

tag: day

tag: ffu

value: female


title: CC003d5_5

tag: agent

value: mouse-adapted H3N2 virus

tag: Sex


title: w4_Tak1f_f_Ripk1D138N_D138N_rep2


title: Sample 144_WT.2R


title: Sample 141_WT.1L


title: CC003d5_4

tag: strains


title: Sample 142_WT.1R


title: WT iTreg 24 h

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

description: Gene expression after 24 h in iTreg cell differentiation condition of wild type naive CD4+ T cells.

hyb_protocol: Using Gene Expression Hybridiation kit (Agilent), 600 ng of Cy3-labelled cRNA (Cy3 incorporation > 6) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, samples were hybridized to SurePrint G3 Mouse GE microarray kit 8x60k (G4852A, Agilent) for 17 hours at 65°C, rotating in hybridization oven (G2545A , Agilent) at 10 rpm.  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 (G2539A) using a setting AgilentG3_GX_1color (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE１_1010_Sep10, QC metric GE１_QCMT_Sep10, and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Output data were further analyzed with GeneSpring GX 12.6.1 with a default setting, with Prcentile=75, to generate values of normalized signal intensity.

source_name: In vitro induced Treg (iTreg) of wild type cells, 24 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mni kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNAiso PLUS (TAKARA). Samples were further cleaned using an NucleoSpin RNA Clean-up XS (MACHEREY-NAGEL). RNA was quantified using a Quantus fluorometer (Promega) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary naïve CD4+ T cells were cultured for 24 h in RPMI1640 medium supplemented with plate-coated anti-CD3 (clone 2C11, 2 μg/ml), anti-CD28 (clone 57.31, 0.5 μg/ml) antibodies, 2-Mercaptoethanol (Invitrogen, 55 μM), 10% fetal bovine serum, and further supplemented with anti-IFN-γ (clone R4-6A2, 1 μg/ml), anti-IL-4 (clone 11B11, 1 μg/ml) antibodies, IL-2 (10 ng/ml, PeproTech) and recombinant human TGF-β1 (0.2 or 0.5 ng/ml, BioLegend).

tag: cell subset

value: iTreg cells

value: Wild type


title: Foxp3-KO iTreg 24 h

description: Gene expression after 24 h in iTreg cell differentiation condition of Foxp3-KO naive CD4+ T cells.

source_name: In vitro induced Treg (iTreg) of Foxp3-KO cells, 24 h

value: Foxp3 knockout


title: Nr4a-TKO iTreg 24 h

description: Gene expression after 24 h in iTreg cell differentiation condition of Nr4a-TKO naive CD4+ T cells.

source_name: In vitro induced Treg (iTreg) of Nr4a-TKO cells, 24 h

value: Nr4a triple knockout


title: w4_Tak1f_f_rep4

value: Liver


title: CC004d3_1


title: Macaque_tibia_T2_ACTTGA

city: Sheffield

first: Ning

last: Wang

address: Beech Hill Road

institute: University of Sheffield

description: processed data file: Macaque_T.profiling-table.txt

data_processing:
Illumina HiSeq Control Software 2.2.38 used for basecalling
Mapping of reads to reference sequences was performed using BWA-MEM (version 0.7.10-r789)
Sequencing reads were counted on gene models with the HTSeq-count program (the –s flag set to ‘no’).
Differential gene expression was analysed with the R package edgeR v. 3.16.5.
Genome_build: MacaM genome assembly (https://www.unmc.edu/rhesusgenechip/index.htm) and its corresponding gene annotations
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Macaca mulatta

extract_protocol:
To obtain highly enriched populations of osteocytes, tibias of mouse and rat were cut to expose the metaphysis and centrifuged briefly to remove bone marrow (1500g, 30 sec).  Calvarial samples were obtained from the rodents with scissors, removing the sutures and avoiding any marrow spaces (diploe). Samples were obtained from the Macaque bones with a hacksaw irrigated with normal saline.  All samples were dissected free of periosteum and accessible surfaces were scraped with a scalpel. They were then immersed briefly in a 1mg/ml solution of collagenase (Sigma Aldrich) for 3-5 minutes at 37°C to remove any adherent surface cells.  Samples were then washed in saline before being snap frozen by complete submersion in liquid nitrogen and then stored at -80˚C.  Bone samples were pulverised using a mikro-dismembrator-S (Braun Biotech International GmbH Melsungen, Germany), in which the bone is shaken in a robust PTFE mill chamber with an 8mm tungsten carbide ball (both cooled in liquid nitrogen before use, and again after adding the bone pieces, before agitation).  The mill with tissue sample was placed within the mikro-dismembrator-S and set to shake at 2500rpm for 45 seconds.  The weight of the fine bone powder was recorded and it was stored for RNA extraction. 1ml of Trizol Reagent (Ambion) was added per 125mg of pulverized tissue (typical tissue amounts 350-500mg); samples were incubated in Trizol reagent for 10 minutes at room temperature.  Samples were centrifuged at 500g for 5 minutes at 4˚C, the supernatant was removed carefully to ensure no debris was transferred. 0.3ml of chloroform was added to each 1ml of Trizol reagent, the sample was thoroughly mixed and allowed to incubate at room temperature for 5 minutes.  The samples were centrifuged at 12,000g for 20 minutes at 4˚C.  The colourless upper phase was collected and transferred to a separate tube, to which an equal volume of 70% ethanol was added and incubated at room temperature for 10 minutes.    The samples were then applied to spin cartridges from TRIzol Plus RNA purification kit (Ambion) following the manufactures instructions using the optional On-Column PureLink DNase (Invitrogen) treatment step.  Samples were quantified using spectrophotometry (NanoDrop Thermo) and quality measure using a Bioanalyzer (Agilent).  Only RNA with a RNA integrity number (RIN) above 8 was stored in -80 ˚C and used for RNA-Seq. Samples used for analysis were one long bone and skull pair pooled from two rats, two long bone and skull pairs each pooled from 3 mice, and 3 long bone and skull pairs each from individual macaques.
cDNA library preparation and sequencing were performed by Eurofins Genomic (Ebersberg, Germany). From the total RNA sample, poly(A)+ RNA was enriched and randomized primer was used for first strand cDNA synthesis.

value: 4-6 month

value: tibia

value: osteocyte


title: w4_Tak1f_f_Ripk1D138N_D138N_rep1


title: Macaque_calvaria_T1_CGATGT

value: calvaria


title: Sample 140_SCID.4R

source_name: SCID_Naive_49_cecal tissue

value: SCID

value: Naive

value: cecal tissue


title: Sample 138_SCID.3R

value: 8 weeks


title: w4_Tak1f_f_rep3

value: 4 weeks


title: Sample 139_SCID.4L


title: CC004cd3_2

value: ctrl


title: Macaque_tibia_G4_TAGCTT

description: processed data file: Macaque_G.profiling-table.txt


title: CC003d5_1

value: female


title: CC003d3_5

value: mouse-adapted H3N2 virus


title: Sample 137_SCID.3L


title: Macaque_calvaria_G3_TGACCA


title: CC003d3_4


title: Sample 136_WT.7R

source_name: WT_Naive_49_cecal tissue

value: WT


title: Macaque_tibia_G2_GATCAG


title: CC003d5_3


title: CC003d3_2


title: Macaque_calvaria_G1_TTAGGC


title: CC003d3_1


title: Bisulfite-seq TetDKO-2

description:
A008_ACTTGA
A009_GATCAG

data_processing:
Reads were mapped on mixed reference sequence comprised of mouse mm10 and Enterobacteria phage lammbda using program BMap.
Alignments exported from BMap were summarized into a graph file by MPTC.
The methylation levels and read coverage were exported by MethExport
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Tet2/Tet3-deficient B cells

extract_protocol:
Genomic DNA was isolated from B cell subsets with Dneasy Blood & Tissue Kit (Qiagen)
tPBAT protocol version 1.0 (Miura F. et al Nucleic Acid Research (2019), 47, e85)

tag: strain

tag: genotype/variation

value: Primary B cells

tag: passages

value: Freshly isolated from spleen


title: Sample 135_WT.7L

tag: genotype


title: Sample 134_WT.6R


title: Bisulfite-seq TetDKO-1

description:
A006_GCCAAT
A007_CAGATC

tag: cell type


title: Sample 133_WT.6L

tag: strain background


title: Bisulfite-seq CTL-2

description:
A004_TGACCA
A005_ACAGTG

source_name: control B cells

value: control


title: CC003cd3_5

source_name: lung


title: UM-SCC-74a (2Gy)

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

description: UM-SCC-74a (2Gy) - Base of tongue squamous cell carcinoma (cell line) - HPV-negative - Irradiated: 2 Gy

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the UCSC ref_gene annotation combined with that of HPV16 (from NC_001526.2 ref_seq)
Genome_build: Combined hg19 and HPV16 (NC_001526.2)
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

growth_protocol: The novel cell lines CU-OP-17 and CU-OP-20 were derived from tonsil tumour biopsies that were obtained from patients prior to treatment at Cardiff and Vale University Health Board, from March 2015 to August 2016.   The study was conducted with NHS Research Ethics Committee approval: Research Ethics Committee for Wales 13/WA/0002, with written consent of patients. The study was performed in accordance with the Declaration of Helsinki.   CU-OP cell lines (CU-OP-2, -3, -17 and -20) were growing in GMEM media with additional supplements and 60 Gy irradiated 3T3 fibroblasts, which were removed prior to RNA extraction (described in detail in"Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus" by Pirotte et al).   The remaining cell lines of this study were grown in DMEM with 10% Fetal Bovine Serum: UM-SCC-47 (HPV-positive), UM-SCC-6 (HPV-negative), UM-SCC-4 (HPV-negative), UM-SCC-19 (HPV-negative), UM-SCC-74a (HPV-negative), cell lines were obtained from Professor Thomas Carey (University of Michigan, USA). UPCI-SCC-90 (HPV-positive) was purchased from DSMZ (Braunschweig, Germany). All cell cultures were incubated at 37°C in 5% CO2.

extract_protocol: Cells (non-irradiated and irradiated with 2 Gy) were collected 24 h after treatment. RNA was extracted with QiaAMP RNA Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Wales Gene Park (Cardiff University, UK) performed the RNA transcriptome sequencing. Library preparation was performed by using the Illumina® TruSeq® Stranded Total RNA with Ribo-Zero Gold™ kit (Illumina Inc.) following manufacturer’s instructions. On the Illumina® HiSeq2500 in high-output mode, a 75-base paired-end dual index read format was used

treatment_protocol: 20 samples (10 non-irradiated and 10 irradiated with 2 Gy and collected after 24 h)

tag: hpv status

value: HPV-negative

tag: p53 status

value: p53 wild-type

value: irradiated with 2 Gy


title: UM-SCC-19 (2 Gy)

description: UM-SCC-19 (2 Gy) - Base of tongue squamous cell carcinoma (cell line) - HPV-negative - Irradiated: 2 Gy

value: p53 mutant


title: CC003cd3_4


title: Bisulfite-seq CTL-1

description:
A002_CGATGT
A003_TTAGGC


title: Sample 132_SCID.1R

source_name: SCID_chronic stress_47_cecal tissue

tag: age

tag: treatment

value: chronic stress


title: CC003cd3_2


title: UM-SCC-6 (2 Gy)

description: UM-SCC-6 (2 Gy) - Base of tongue squamous cell carcinoma (cell line) - HPV-negative - Irradiated: 2 Gy


title: Sample 131_SCID.1L

value: SCID

tag: experiment day

tag: sample type


title: UM-SCC-4 (2 Gy)

description: UM-SCC-4 (2 Gy) - Tonsil squamous cell carcinoma (cell line) - HPV-negative - Irradiated: 2 Gy


title: CC003cd3_1

tag: day

tag: ffu


title: maize_ligular_region_mRNA_SEQ_Sdw3_rep3

city: Beijing

first: Hongchao

address: No.2 Yuanmingyuan West Road

department: Crop Genetics and Breeding

institute: China Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads analyzed using Bcl2Fastq
Raw data can be filtered according to NEBNext Ultra RNA Library Prep Kit. The RNA 5' Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; the RNA 3' Adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Clean data were mapped to the maize genome with TopHat (V2.1.0)
The Cufflinks package was used to assemble transcripts, compare and merge assembles, and identify differentially expressed genes (DEGs).
Genome_build: Zea mays B73 RefGen_v3
Supplementary_files_format_and_content: log2(fold_change（Sdw3/N18)

organism: Zea mays

source_name: ligular region

extract_protocol:
Total RNA was extracted from the samples using a Plant RNA Isolation Kit (Waryong, China) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: developing ligular region of leaf8 and leaf9

tag: developmental stage

tag: cultivar


title: w4_Tak1f_f_rep1

value: Liver


title: w4_Tak1f_f_rep2


title: maize_ligular_region_mRNA_SEQ_Sdw3_rep2


title: CU-OP-20 (2 Gy)

description: CU-OP-20 (2 Gy) - Tonsil squamous cell carcinoma (cell line) - HPV-positive - Irradiated: 2 Gy

value: HPV-positive

tag: agent