title: RNA.P6 rep2

description:
jrbrady_RNARibo_intCt.txt
jrbrady_RNARibo_l2tpm.txt

data_processing:
Sequence reads were quantified using salmon version 0.11.3 and transcript target consisting of phaffi T0 transcripts and a P6 CDS transcript.
NextSeq500 using v3 chemistry. Software: Control v2.2.0.2, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Genome_build: Komagataella phaffi WT (PRJNA304977) with inserted transgenes where indicated
Supplementary_files_format_and_content: jrbrady_RNARibo_intCt.txt.gz is tab delimited integer count data with rows identified by geneID and symbol
Supplementary_files_format_and_content: jrbrady_RNARibo_l2tpm.txt.gz is tab delimited lpg2 tpm data with a plus1 offset with rows identified by geneID and symbol
Supplementary_files_format_and_content: P4.wig_fw.wig.gz is a wiggle format file of depth by position for forward strand reads
Supplementary_files_format_and_content: P4.wig_rc.wig.gz is a wiggle format file of depth by position for reverse strand reads
Supplementary_files_format_and_content: P6.wig_fw.wig.gz is a wiggle format file of depth by position for forward strand reads
Supplementary_files_format_and_content: P6.wig_rc.wig.gz is a wiggle format file of depth by position for reverse strand reads

extract_protocol:
KAPA HyperPrep kit (Roche, Basel, SUI)
Cell samples from cultures expressing P[4] or P[6] were transferred to a shake-flask containing 500 mL of pre-warmed fresh BMMY media to achieve an OD600 = 0.5. Cell harvest, cell lysis, and recovery of ribosome footprints were performed as described previously (Taggart et al., Cell Syst. 2018). Samples were split following lysis for total RNA-Seq and ribosome profiling (Ribo-Seq).


title: F_P7_normal_CD31_1_DC21_C12

status: Public on May 05 2021

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
scRNA-Seq: plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: tissue

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Proliferative EC

tag: mousename

tag: coverage

tag: number of genes

tag: treatment

value: normal


title: F_P7_normal_CD31_1_DC21_P4

value: Venous EC


title: Gata3_Day3.7.mTE_2

city: Exeter

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

data_processing:
Trim-Galore
STAR
FeatureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts_raw.txt: Raw counts text file.

organism: Homo sapiens

source_name: Blastoid

growth_protocol: Frozen human blastocysts (E5 or E6) were thawed and cultured in N2B27 medium under mineral oil. The majority of embryos were cultured for 24 hours for development to late blastocysts (E6 or E7). Human naïve pluripotent stem cells (HNES1-GATA3:mKO2) [Ge Guo et al., 2021] or niPSC [Bredenkamp Nicholas et al.,2019] were cultured in PXGL on MEF. Dissociated human naïve pluripotent stem cells were cultured in a low attachment 96-well plate in N2B27 supplemented with 1.5uMPD03 and 1uMA83 and 10uM Y-27632 for 44h. The formed aggregates were transferred in N2B27 supplemented with 0.5uM A83. After 18h, they were transferred to N2B27 to form blastocyst-like structure.

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen.
The Smart-Seq2 library was prepared as described in Picelli S et al. 2014.

treatment_protocol: The zona pellucida was removed using acid Tyrode’s solution. Human embryos and human blastocyst model were moved to filtered M2 drop and cut mTE manually using glass pipettes. mTE and the other part containing ICM and pTE were transferred to a drop of Accutase or TrypLE respectively using glass capillary or Pasteur pipette and incubated for 7-10 min at 37 oC or room temperature. Then mTE and ICM with pTE were transferred to a drop of filtered M2 respectively and dissociated by repetitive pipetting using a finely drawn Pasteur pipette or glass capillary of which diameter is just larger than a cell.

value: Blastoid

tag: lineage

value: Trophectoderm

value: mural

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: RNA.P6 rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

organism: Komagataella phaffii

source_name: bulk yeast cell culture

growth_protocol: BMGY containing 4% (v/v) glycerol was inoculated from a glycerol stock to an initial OD600 of 0.1 in a 24-well culture plate (Corning, Cat. # P-DW10ML24CS, Corning, NY) and cultured at ambient temperature and 600 rpm shaking. After 24h of biomass accumulation, cells were pelleted and resuspended in BMMY, containing 3% (v/v) methanol as both a carbon source and for induction of heterologous gene expression, for an additional 16h.

tag: protein expressed

tag: clone id


title: RNA.P6 rep1


title: F_P7_normal_CD31_1_DC21_L20

value: Early Car4- capillaries


title: RNA.P4 rep3

data_processing:
Sequence reads were quantified using salmon version 0.11.3 and transcript target consisting of phaffi T0 transcripts and a P4 CDS transcript.
NextSeq500 using v3 chemistry. Software: Control v2.2.0.2, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Genome_build: Komagataella phaffi WT (PRJNA304977) with inserted transgenes where indicated
Supplementary_files_format_and_content: jrbrady_RNARibo_intCt.txt.gz is tab delimited integer count data with rows identified by geneID and symbol
Supplementary_files_format_and_content: jrbrady_RNARibo_l2tpm.txt.gz is tab delimited lpg2 tpm data with a plus1 offset with rows identified by geneID and symbol
Supplementary_files_format_and_content: P4.wig_fw.wig.gz is a wiggle format file of depth by position for forward strand reads
Supplementary_files_format_and_content: P4.wig_rc.wig.gz is a wiggle format file of depth by position for reverse strand reads
Supplementary_files_format_and_content: P6.wig_fw.wig.gz is a wiggle format file of depth by position for forward strand reads
Supplementary_files_format_and_content: P6.wig_rc.wig.gz is a wiggle format file of depth by position for reverse strand reads


title: Gata3_Day3.7.mTE_1


title: Gata3_Day3.7.pTEICM_27

value: polar


title: RNA.P4 rep2


title: F_P21_normal_mesench_1_DC21_F12

value: Late Car4- capillaries


title: F_P7_normal_CD31_1_DC21_C20

value: Car4+ capillaries


title: P6-A3C

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179024

data_processing:
NextSeq500 using v3 chemistry. Software: Control v2.2.0.2, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequenced reads were aligned and quantified using STAR v2.5.3a and RSEM v1.3.0.
Expression was visualized using log2(Fragments per Kilobase of Transcript per Million Mapped Reads + 1) values.
Genome_build: Komagataella phaffi WT (PRJNA304977) with inserted transgenes where indicated
Supplementary_files_format_and_content: jrbrady_RNAseq_intCt.txt.gz is tab delimited integer count data with rows identified by geneID and symbol
Supplementary_files_format_and_content: jrbrady_RNAseq_l2fpkm.txt.gz is tab delimited lpg2 fpkm data with a plus1 offset with rows identified by geneID and symbol

growth_protocol: BMGY containing 4% (v/v) glycerol was inoculated from a glycerol stock to an initial OD600 of 0.1 in a 24-well culture plate (Corning, Cat. # P-DW10ML24CS, Corning, NY) and cultured at ambient temperature and 600 rpm shaking. After 24h of biomass accumulation, cells were pelleted and resuspended in BMMY, containing 1.5% (v/v) methanol as both a carbon source and for induction of heterologous gene expression, for an additional 24h.

extract_protocol:
Cells were first digested in digestion buffer (50 mM EDTA, 500 mM sorbitol, pH 7.4) supplemented with 0.1% (v/v) 2-Mercaptoethanol and Zymolyase (Zymo Research, Irvine, CA) for 25 min at 30°C and 100 rpm shaking. Lysis and RNA purification was then performed using the RNeasy kit (Qiagen, Cat #74104). RNA quality was analyzed to ensure RNA Quality Number >7.
KAPA HyperPrep kit (Roche, Basel, SUI)


title: P6-A3B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179016


title: P4-A1A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179013


title: Gata3_Day4.6.pTEICM_10

value: Primitive Endoderm

value: 4 days after stem cells seeded to form cell aggregates


title: RNA.P4 rep1


title: Gata3_Day3.7.pTEICM_26


title: F_P21_normal_mesench_2_DC21_O22


title: F_P7_normal_CD31_1_DC21_O1


title: Gata3_Day4.6.pTEICM_8


title: F_P7_normal_CD31_1_DC21_H4


title: P4-A3B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179015


title: P8-6C

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179020


title: P4-A3C

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179023


title: P4-A3A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179007


title: Gata3_Day4.6.pTEICM_7


title: L0615_TMZ_RNAseq

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

description:
POL_F04_0001_P01_V21_S6_1
l0615_tmz_rnaseq_spheres

data_processing:
The sequenced paired-end reads were mapped to hg38 genome using tophat2 aligner with the default parameters. The counts were computed with Htseq software.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files were generated using coverage function from GenomicAlignments Bioconductor;   expression.matrix.txt file is a tab-delimited text file including TPM values for each Sample

molecule: polyA RNA

growth_protocol: Sphere forming assay: GBM-derived stem cells (L0125, L0512, L0615, L0627) were seeded at a low density (3000 viable cells/cm2) onto non-adherent plates and cultured in DMEM/F-12 medium, supplemented with 2% B27 (Gibco Invitrogen, Basel, Switzerland), 20 ng/ml rh bFGF (Miltenyi Biotec, Bergisch Gladbach, Germany), 20 ng/ml rh EGF (StemCell Technologies, Vancouver, BC, Canada), 0.0002% heparin (StemCell Technologies, Vancouver, BC, Canada) and antibiotics (Gibco Invitrogen, Basel, Switzerland). Cells were fed every 3 days by adding 25% of the medium.

extract_protocol:
Total cellular RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and purified using RNeasy columns according to the manufacturer’s instructions. The integrity of RNA was checked using the Agilent's 2100 Bioanalyzer. The same amount of RNA from two independent experiments were used (total amount - 500ng of RNA).
In total, 12 strand-specific polyA enriched RNA libraries were prepared using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Kapa Biosystems, Wilmington MA, USA). Libraries were run in the rapid run flow cell.

treatment_protocol:
Sphere differentiation: 6-day spheres were treated with 100 ng/ml BMP4 for 4 days (with fresh BMP4 was added every two days).
Treatment of spheres with TMZ: control (kept for 6-day) or BMP4-differentiated spheres (for 4 days) were treated with 500 mM TMZ for the next 3 days. As DMSO induced differentiation of embryonic stem cells, for the most experiments TMZ was dissolved in deionized water. A stock solution 30.9 mM (6 mg/ml) of TMZ was prepared.

tag: cell line

value: GBM-derived stem cells

value: Temozlomide

tag: egfr status

value: high


title: F_P7_normal_CD31_1_DC21_I18

tag: tissue

value: distal lung

tag: sequencing run

value: F

value: endothelial


title: P4-A1B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179021


title: P8-6A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179004


title: P6-14C

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179019


title: Gata3_Day4.6.pTEICM_9

value: Epiblast


title: P6-14B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179011


title: P6-14A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179003


title: F_P7_normal_CD31_1_DC21_A8

tag: gender

tag: plate

value: normal


title: Gata3_Day4.6.pTEICM_5

value: Blastoid

value: Trophectoderm


title: P6-A3A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179008


title: P4-3C

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179018


title: Gata3_Day4.6.pTEICM_4


title: F_P7_normal_CD31_1_DC21_N21

tag: well

tag: timepoint


title: Gata3_Day4.6.pTEICM_3


title: WT-B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179009


title: F_P7_normal_CD31_1_DC21_A12

tag: cell type

tag: cell subtype

value: Proliferative EC


title: F_P7_normal_CD31_1_DC21_F6

tag: mousename

tag: coverage


title: Gata3_Day3.7.pTEICM_25

value: 3 days after stem cells seeded to form cell aggregates


title: WT-A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179001


title: P8-6B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179012


title: F_P7_normal_CD31_1_DC21_H23

value: Early Car4- capillaries

tag: number of genes

tag: treatment


title: Gata3_Day3.7.pTEICM_24

tag: lineage

value: polar

tag: time point


title: F_P7_normal_CD31_1_DC21_B15


title: M_GF_R2_L1

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
smallRNA processing: The function SamToFastq, included in the Picard tool package, was used to convert the original BAM format to FASTQ format (for the raw data which was not already in FASTQ format), on which a quality control was performed, using FastQC
smallRNA processing: Cutadapt, quality trimming (20), read length filtration 18 - 38 nt
smallRNA processing: Bowtie2 in combination with SAMtools view were used for tRNA and rRNA trimming and potato and P. infestans sRNA filtering to exclude the reads from the other genome for the different datasets, using 0 mismatches allowed per seed against each Fasta filter
smallRNA processing:  SamToFastq converted the files to fastq
smallRNA processing: Seqtk was applied to convert the FASTQ files to FASTA.
Degradome processing: Raw RNA reads from degradome libraries were adaptor- and quality trimmed with Cutadapt
Degradome processing: Seqtk was applied to convert the FASTQ files to FASTA.
The sRNA and degradome fasta files and  were analyzed in PAREsnip2.
PAREsnip output data was imported in R where PAREsnip2 replicates were merged and duplicated targets were discarded.
Resulting datasets were analyzed in our machine learning script (https://github.com/kristianHoden/degradome). False positives were discarded
The datsets were sorted in list according to their Normalized Fragment Abundance (NFA) and targeting transcriptome
Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1)
fasta format of small RNA and degradome libraries
Genome_build: Solanom tuberosum genome v4.04, Phytophthora infestans genome (ASM14294v1)
Supplementary_files_format_and_content: pinfDown - contain the datasets with targets in P. infestans with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: pinfUp - - contain the datasets with targets in P. infestans with increased NFA of the targets upon infection
Supplementary_files_format_and_content: potDown - contain the datasets with targets in potato with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: potUp - - contain the datasets with targets in potato with increased NFA of the targets upon infection
Supplementary_files_format_and_content: rDown - contain the datasets with targets in resistance (R) genes in potato with decreased NFA of the targets upon infection
Supplementary_files_format_and_content: rUp - contain the datasets with targets in resistance (R) genes in potato with increased NFA of the targets upon infection

organism:
Solanum tuberosum
Phytophthora infestans

source_name: Mycelia

growth_protocol: P. infestans were maintained at 20 °C on rye agar medium supplemented with 2 % sucrose (Caten & Jinks 1968), rifampicin (10 μg ml−1), and pimaricin (10 μg ml−1). Transgenic lines of P. infestans isolate 88069 were maintained as above, but with the addition of the antibiotic geneticin (G418; 10 μg ml−1) to the medium.

extract_protocol:
Mycelia were harvested and flash frozen in liquid nitrogen.
Degradome library preparation was performed as earlier outlined (Sanz-Carbonell et al. 2020). 10 libraries were sequenced at SciLifeLab (Uppsala, Sweden) using HiSeq2500 rapid SR50 technologies.

treatment_protocol: To prepare mycelium samples for RNA isolation, P. infestans was grown in liquid pea medium (Whisson et al. 2005b) for 5 d at 20 °C. Mycelium was harvested by filtration, snap frozen in liquid nitrogen, and stored at −70 °C until required.

tag: p. infestans strain

tag: dpi

value: Mycelia


title: M_GF_R1_L2


title: M_GF_R2_L2


title: F_P7_normal_CD31_1_DC21_M20

value: Late Car4- capillaries


title: Gata3_Day3.7.pTEICM_22

value: Primitive Endoderm


title: Gata3_Day3.7.pTEICM_21


title: M_88_R2_L2


title: P4-3B

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179010

tag: protein expressed

tag: clone id


title: Gata3_Day3.7.pTEICM_20

tag: tissue


title: M_88_R2_L1


title: M_88_R1_L2


title: F_P7_normal_CD31_1_DC21_O18

tag: sequencing run

tag: gender


title: siSTEAP1

type: RNA

city: Sapporo

first: Hajime

last: Nakamura

state: Hokkaido

address: South-1, West-16, Chuo-ku

department: Department of Medical Oncology

country: Japan

institute: Sapporo Medical University School of Medicine

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze
For the normalization it uses the average of housekeeping genes: B2M and RPLP0
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: HepG2 cells transfected with siRNA targeting STEAP1

label_protocol: Total RNA was reverse-transcribed using an RT² First Strand Kit. PCR array was performed using RT² Profiler™ PCR Array Human MYC Targets (PAHS-177Z; Qiagen).

growth_protocol: Cells were cultured in DMEM containing 10% fetal bovine serum (FBS), 2μM L-glutamine and 1% penicillin-streptomycin

extract_protocol: Total RNA

treatment_protocol: HepG2 cells were seeded into 6-well plates and cultured for 24 h. Subsequently, cells were transfected with siRNA targeting human STEAP1 (siSTEAP1) or control siRNA (Control) and incubated for 72h.

value: Human hepatoma cell line

tag: cell line

value: transfected with siRNA targeting STEAP1


title: M_GF_R1_L1


title: M_88_R1_L1

extract_protocol:
Mycelia were harvested and flash frozen in liquid nitroMycelia were harvested and flash frozen in liquid nitrogen. gen.
Degradome library preparation was performed as earlier outlined (Sanz-Carbonell et al. 2020). 10 libraries were sequenced at SciLifeLab (Uppsala, Sweden) using HiSeq2500 rapid SR50 technologies.


title: F_P21_normal_mesench_1_DC21_K14

tag: plate

tag: well

tag: timepoint


title: P4-3A

description:
jrbrady_RNAseq_intCt.txt.gz
jrbrady_RNAseq_l2fpkm.txt.gz
d179002


title: Gata3_Day3.7.pTEICM_19


title: B_GF_R2_L1

source_name: Infected leaves

growth_protocol: Potato plants were grown in-vitro at 22°C with a 16-h photoperiod on Murashige-Skoog (MS) medium (Duchefa Biochemie B.V., Amsterdam, Netherlands), supplemented with 2% (w/v) sucrose and 0.3% (w/v) gelrite (Duchefa). After 3 weeks plants were transferred to pots with soil in a growth chamber with the same light and temperature regime. P. infestans were maintained at 20 °C on rye agar medium supplemented with 2 % sucrose (Caten & Jinks 1968), rifampicin (10 μg ml−1), and pimaricin (10 μg ml−1). Transgenic lines of P. infestans isolate 88069 were maintained as above, but with the addition of the antibiotic geneticin (G418; 10 μg ml−1) to the medium.

extract_protocol:
Inoculated leaves were harvested and flash frozen in liquid nitrogen.
Degradome library preparation was performed as earlier outlined (Sanz-Carbonell et al. 2020). 10 libraries were sequenced at SciLifeLab (Uppsala, Sweden) using HiSeq2500 rapid SR50 technologies.

treatment_protocol: Sporangia were harvested from 14 d old agar cultures by flooding cultures with water, and rubbing the culture with a glass rod. Sporangial suspensions were decanted, counted on a haemocytometer, and adjusted to 5 × 10^4 sporangia ml^−1. Attached leaflets were inoculated with a 10 μl droplet (500 sporangia) on either side of the leaf midrib, 4 weeks post transfer to soil from in-vitro conditions.

tag: potato cultivar

value: Bintje

value: Infected leaves


title: F_P7_normal_CD31_1_DC21_K13

value: distal lung

value: F

tag: cell type

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage


title: F_P7_normal_CD31_1_DC21_A17

value: endothelial

tag: number of genes

tag: treatment

value: normal


title: F_P7_normal_CD31_1_DC21_H8


title: B_GF_R1_L2

tag: p. infestans strain

tag: dpi


title: B_GF_R2_L2


title: B_GF_R1_L1


title: control

description: Control

source_name: HepG2 cells transfected with control siRNA

value: transfected with control siRNA


title: Gata3_Day4.6.pTEICM_2

value: Blastoid

tag: lineage

value: Epiblast

tag: time point

value: 4 days after stem cells seeded to form cell aggregates


title: B_88_R2_L1

tag: tissue


title: F_P7_normal_CD31_1_DC21_N14

tag: sequencing run

tag: gender


title: Gata3_Day4.6.pTEICM_1

value: polar


title: B_88_R2_L2


title: all 11388 2

extract_protocol:
Inoculated leaves were harvested and flash frozen in liquid nitrogen.
sRNA libraries were generated using Illumina small RNA sample preparation kit. Libraries were prepared by SciLife sequencing platform (Stockholm, Sweden) under their in-house conditions and sequenced using Illumina HiSeq 2500

value: Sarpo Mira


title: B_88_R1_L1


title: Gata3_Day4.5.mTE_4

value: Trophectoderm

value: mural


title: F_P7_normal_CD31_1_DC21_O13

tag: plate

value: Proliferative EC


title: B_88_R1_L2


title: all 88069 1


title: Gata3_Day4.5.mTE_2


title: F_P7_normal_CD31_1_DC21_M17

tag: well

value: Early Car4- capillaries


title: all 88069 2


title: Gata3_Day3.7.pTEICM_18

value: Transitioning

value: 3 days after stem cells seeded to form cell aggregates


title: Mut5_2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
We used Edge-Pro for mapping and quantification and qualimap for quality control
Noiseq was used for data normalization
Genome_build: CP011110.1 and NZ_CP011937.1
Supplementary_files_format_and_content: tab-delimited excel files include Log2FC of the comparison of interactions, with p-value

organism: Bacillus amyloliquefaciens

source_name: FZB42 mut GlpK

extract_protocol:
Single colonies of PCL1606 and FZB42 WT and the GlpK mutant were grown overnight in LB medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 µl were spotted on King B plates alone and in interaction between PCL1606 and the Bacillus strains. Cultures were grown for 24h at 30°C. After that, colonies were recovered and stored at -80C. The collected cells were resuspended and homogenized by passing through a 25 5/8 G needle in BirnBoim A (20% sucrose, 10mM tris-HCl pH 8, 10mM EDTA and 50mM NaCl). Lysozyme (10 mg/ml) was added and incubated 30 min at 37C. After disruption, suspensions were centrifuged, and pellets were resuspended in Trizol reagent (Invitrogen). Total RNA extraction was performed as indicated by the manufacturer. Removal of DNA was carried out by in-column treatment with the rDNAse included in the Nucleo-Spin RNA Plant (Macherey-Nagel) following instructions from the manufacturer. Integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: B. amyloliquefaciens FZB42

tag: genotype/variation

value: FZB42 mut GlpK


title: Gata3_Day4.5.mTE_5


title: FZB42vsPCL1606_1

source_name: Interaction WT

value: Interaction WT


title: Mut5_1


title: F_P7_normal_CD31_1_DC21_G17

value: distal lung

value: F

tag: timepoint

tag: cell type

value: endothelial

value: Car4+ capillaries


title: FZB42_2

source_name: B. amyloliquefaciens FZB42

value: WT


title: Gata3_Day4.5.pTEICM_29

value: Blastoid

value: Epiblast

value: 4 days after stem cells seeded to form cell aggregates


title: FZB42vsPCL1606_2


title: F_P7_normal_CD31_1_DC21_K21

tag: cell subtype

tag: mousename

value: normal


title: F_P7_normal_CD31_1_DC21_J22

tag: coverage

tag: number of genes


title: FZB42_1


title: F_P7_normal_CD31_1_DC21_E23

tag: treatment


title: PCL1606vsFZB42_1

organism: Pseudomonas chlororaphis

value: P. chlororaphis PCL1606


title: PCL1606vsFZB42_2


title: Gata3_Day3.7.pTEICM_17

value: polar


title: all 11388 1

tag: potato cultivar

value: Sarpo Mira

tag: p. infestans strain

tag: dpi

value: Infected leaves


title: F_P7_normal_CD31_1_DC21_P11

tag: tissue

value: Early Car4- capillaries


title: Gata3_Day3.7.pTEICM_16

tag: lineage

value: Trophectoderm

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_L3

tag: sequencing run

tag: gender

tag: plate


title: PCL1606_2

source_name: P. chlororaphis PCL1606

tag: strain

tag: genotype/variation


title: PCL1606_1


title: Gata3_Day3.7.pTEICM_15


title: Gata3_Day4.5.mTE_1

value: mural


title: PHU_PABPC1_3T

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to human reference genome hg38 by HISAT2 aligner (version 2.1.0)
Mutation calling was performed by SAMtools (version 1.9) and bcftools (version 1.9)
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bam2wig (version 1.5)

source_name: Colon

extract_protocol:
Amplicon sequencing was specifically targeted on two candidate genes: FAM104A and PABPC1 using primer sets ACAACCCCCTCTGTTCCCTCT/ATGGTCTGGCTCAAGCTGCCT for FAM104A and AGCAAATGTTGGGTGAACGGC/TTCTTCGGTGAAGCACAAGTTTC.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

tag: patient

value: Patient 3

tag: sample

value: tumor sample

tag: target gene

tag: treatment enzyme

value: PHU


title: PHU_PABPC1_3M

value: metastasis sample


title: F_P7_normal_CD31_1_DC21_A3

value: distal lung

value: F

tag: well

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Car4+ capillaries

tag: mousename

tag: coverage

tag: number of genes


title: Gata3_Day3.7.pTEICM_14

tag: tissue

value: Blastoid

tag: lineage

tag: time point


title: PHU_PABPC1_2T

value: Patient 2


title: F_P7_normal_CD31_1_DC21_K20

tag: sequencing run

tag: gender

tag: plate

tag: treatment

value: normal


title: PHU_PABPC1_2M

tag: patient

tag: sample


title: PHU_FAM104A_2T

tag: target gene

tag: treatment enzyme


title: Gata3_Day3.7.pTEICM_12

value: Epiblast

value: polar


title: F_P7_normal_CD31_1_DC21_O6

tag: well

tag: timepoint

value: Arterial EC I


title: PHU_FAM104A_2M


title: F_P7_normal_CD31_1_DC21_J12

tag: cell type

tag: cell subtype

value: Early Car4- capillaries


title: Gata3_Day3.7.pTEICM_10

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.7.pTEICM_11

value: Trophectoderm


title: PHU_FAM104A_1M

value: Colon

value: Patient 1


title: F_P7_normal_CD31_1_DC21_B7

value: Venous EC

tag: mousename

tag: coverage


title: Gata3_Day4.5.pTEICM_28

tag: tissue

value: 4 days after stem cells seeded to form cell aggregates


title: GRM_PABPC1_3T

value: Patient 3

value: tumor sample

value: GRM


title: GRM_PABPC1_2T


title: F_P7_normal_CD31_1_DC21_C19

value: distal lung

value: F

value: endothelial

tag: number of genes


title: GRM_PABPC1_2M

value: Patient 2

value: metastasis sample


title: GRM_FAM104A_2T


title: PHU_FAM104A_1T

value: PHU


title: F_P7_normal_CD31_1_DC21_M2

value: Late Car4- capillaries

value: normal


title: Gata3_Day4.5.pTEICM_26

value: Blastoid

tag: lineage

value: polar

tag: time point


title: GRM_PABPC1_3M

value: Colon


title: Gata3_Day4.5.pTEICM_25

value: Trophectoderm


title: GRM_FAM104A_1T

value: Patient 1


title: GRM_FAM104A_1M


title: Gata3_Day4.5.pTEICM_24

value: Epiblast

value: 4 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_L4

tag: sequencing run

tag: gender

value: Early Car4- capillaries


title: GRM_FAM104A_2M

value: GRM


title: Gata3_Day4.5.pTEICM_23


title: F_P7_normal_CD31_1_DC21_N9

value: distal lung

tag: plate

tag: treatment


title: ∆yebEFG ESP nalidixic acid Rep1

city: Sevilla

first: Ángela

last: Mérida-Floriano

state: Sevilla

address: Avda. Reina Mercedes 6

department: Genetics

institute: Universidad de Sevilla

data_processing:
Read processing and alignment: The quality of each RNA-seq library was assessed using FastQC v0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The remaining reads of each library were aligned to the corresponding genomes using Bowtie2 v2.2.29 (Langmead & Salzberg, 2012) and alignments were filtered with Samtools v1.3.1 (Li et al., 2009) using MAPQ cut-off of 15. S. Typhimurium ATCC 14028 reads were aligned to the sequences of the published ATCC 14028 chromosome (GenBank CP001363). The complete RNA-seq pipeline used for this study is described in https://github.com/will-rowe/rnaseq.
Quantifying absolute expression levels : Absolute expression levels were calculated as Transcript Per Million (TPM) values (Wagner, Kin, & Lynch, 2012, 2013) and generated for coding genes and  ncRNAs in the chromosome for both 4/74 and ATCC 14028. Based on the values obtained the expression cut-off was set as TPM > 10 for genes and ncRNAs (Kröger et al., 2013).
Supplementary_files_format_and_content: Tab-delimited text files incluse TPM and count values for every gene in each condition

organism: Salmonella enterica

source_name: Salmonella

growth_protocol: All cultures were grown at 37º 200rpm shaking in LB to ESP (OD600nm 2.00) or in LB+Nalidixic acid 8.5ug/ml 4 hours

extract_protocol:
Total RNA was isolated using the Direct-zol RNA MiniPrep Plus kit (Zymo Research). RNA quality and concentration was determined by nanodrop.
cDNA libraries were prepared and sequenced by Vertis Biotechnologie AG (Freising, Germany). Ribodepleted RNA samples were fragmented by ultrasound pulses (4 pulses of 30s each at 4ºC). Oligonucleotide adapter was ligated to the 3’ end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5’ Illumina TruSeq sequencing adapter was ligated to the 3’ end of the antisense cDNA. The resulting cDNA was amplified to about 10-20 ng/ml using a high fidelity DNA polymerase. The cDNA was amplified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis. cDNA samples were pooled in equimolar amounts, size-selected to 200-550 bp and sequenced on an Illumina NextSeq 500 system using 75 bp read length.

value: Bacteria

tag: genotype

value: {delta}yebEFG mutant

value: LB+nalidixic acid 8.5ug/ml 4h


title: ∆yebEFG ESP nalidixic acid Rep2


title: ∆yebEFG ESP nalidixic acid Rep3


title: ∆yebEFG ESP Rep2

value: LB to OD600nm 2.00


title: ∆yebEFG ESP Rep3


title: ∆yebEFG ESP Rep1


title: F_P21_normal_mesench_2_DC21_H21

value: F

value: endothelial


title: Gata3_Day4.5.pTEICM_22


title: WT Nal Rep2

value: Wild type


title: WT Nal Rep3


title: Gata3_Day3.7.pTEICM_9

value: Blastoid

value: Transitioning

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_M12

value: normal


title: Gata3_Day4.5.pTEICM_21

value: Trophectoderm

value: polar


title: WT Nal Rep1


title: F_P21_normal_mesench_2_DC21_J9

value: Late Car4- capillaries


title: Gata3_Day3.7.pTEICM_8


title: WT ESP Rep2


title: F_P21_normal_mesench_1_DC21_N1

value: Car4+ capillaries


title: WT ESP Rep3


title: WT ESP Rep1


title: F_P21_normal_mesench_1_DC21_K3


title: Gata3_Day3.7.pTEICM_7

value: Epiblast


title: F_P7_normal_CD31_1_DC21_C10

value: distal lung


title: F_P7_normal_CD31_1_DC21_G19

value: Arterial EC I


title: Gata3_Day3.7.pTEICM_6


title: FUSR521C_2

first: Bernhard

last: Kuhn

state: Pennsylvania

address: 4401 Penn Ave

institute: Children's Hospital of Pittsburgh

data_processing:
All fastq file were gathered from the sequencer. Quality assurance was performed using FASTQC. All reads were trimmed to remove any nucleotide that fails a phred score < Q20. The trimmed FASTQ files were aligned to the mm10 reference library using RNA STAR.
Quality controlled FASTQ files were aligned to the Ensembl Drosophila genome using the STAR aligner (version 2.5.1). Read summarization was done by feature Counts to produce a matrix of counts.
Differential gene expression analysis between the different conditions was done using DESeq2 using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate, and differentially expressed genes were determined at the 5% threshold. Gene set enrichment analysis was used to assess the statistical enrichment of gene ontologies, and pathways.
Genome_build: Ensembl Drosophila genome using the STAR aligner (version 2.5.1).
Supplementary_files_format_and_content: Tab delimited file of raw read counts

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Adult Drosophila brains were dissected and placed in TRIzol (Ambion; 15596026) and RNA was isolated using a phenol-chloroform extraction method.
500ng of total RNA was used to prepare libraries for sequencing using the Lexogen SENSE mRNA-seq library kit for Ion Torrent. Libraries and amplified for 12 cycles as the final step of library preparation. Before sequencing, small aliquots of this material were quantified by qPCR utilizing the KAPA Library Quantification kit for the Ion Torrent. Quantification data from qPCR was used to balance the barcodes for final pooling before sequencing. Following this final pooling the library pools were sized to a target size of 300bp on a Pippin Prep instrument. The sized libraries were examined on an Agilent High Sensitivity DNA chip, quantified using real-time PCR, and used for sequencing on the Ion Torrent Proton platform.

tag: strain

value: brain

tag: treatement

value: RU486 Drug Food

tag: age

value: Adult Day 8


title: FUSWT_3

value: FUSWT/+


title: FUSWT_1


title: FUSWT_2


title: F_P7_normal_CD31_1_DC21_K16

value: F

tag: well

tag: timepoint

value: endothelial

value: Early Car4- capillaries


title: Gata3_Day3.7.pTEICM_5

value: Blastoid


title: FUSR521C_3


title: FUSR521C_1


title: F_P7_normal_CD31_1_DC21_M7

tag: cell type

tag: cell subtype


title: Gata3_Day3.7.pTEICM_4

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_M5

value: Proliferative EC

tag: mousename

tag: coverage

value: normal


title: L3_R9D11_10Xv3

city: Philadelphia

first: Sylvia

middle: N

last: Michki

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Alignment (STAR-solo)
Cell filtering (scanpy, min_genes=200, max_genes=4100)
Gene filtering (scanpy, min_cells=2)
Normalization (scanpy, ln(1+UMI))
Genome_build: BDGP6.94
Supplementary_files_format_and_content: hdf5 file, containing an anndata object (readable by scanpy) that has the filtered, normalized, log-transformed data matrix inside, along with other related cell-type clustering and projection parameters/values.

source_name: developing central nervous system

growth_protocol: Growth at 27C

extract_protocol:
10X chromium v3 chemistry
Illumina nextera xt library preparation

treatment_protocol: Dissection in Rinaldini’s soln., dissociation at 37C for 1hr in 2mg/mL papain and 2mg/mL collagenase (I), mechanical trituration, FACS sorting into Schneider’s + 10% FBS

tag: developmental stage

value: 3rd instar larva

tag: tissue

value: type-II lineage derived cells and optic lobe cells from the developing 3rd instar larval brain


title: Control_2

value: W1118 Control


title: Gata3_Day3.7.pTEICM_3

tag: lineage

value: Trophectoderm

value: polar

tag: time point


title: Control_1


title: S18 BRSV challenged

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

description: counts.txt

data_processing:
The 3' end of the sequence reads were trimmed for Illumina adapters, low quality reads (quality score <  20), ambiguous nucleotides, and poly-G artefacts resulting from the NextSeq’s two-colour chemistry, using CutAdapt (version 1.18).
The cleaned sequence reads were evaluated for quality using FastQC.
Reads were aligned to the UMD3.1 bovine reference genome and read counts were generated by converting aligned reads into counts per gene using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.6.1b)
Genome_build: UMD3.1
Supplementary_files_format_and_content: TXT file of raw counts table of sequenced reads

organism: Bos taurus

source_name: whole blood

extract_protocol:
Total RNA was extracted using the Tempus™ Spin RNA Isolation Kit (Bio-Sciences LTD, Dublin, Ireland), according to the manufacturer's instructions.
RNA-Seq library preparation was performed using the TruSeq stranded mRNA Kit (Illumina, San Diego, California, USA).

value: BRSV challenged

tag: breed

value: Holstein-Friesian

tag: shed

value: C


title: F_P7_normal_CD31_1_DC21_O8

value: distal lung

tag: sequencing run

tag: gender

tag: plate

tag: number of genes

tag: treatment


title: S17 BRSV challenged

description: counts.txt


title: Gata3_Day4.5.pTEICM_20

value: Epiblast

value: 4 days after stem cells seeded to form cell aggregates


title: S16 BRSV challenged

description: counts.txt


title: Gata3_Day4.5.pTEICM_19


title: F_P21_normal_mesench_1_DC21_O2

value: F

tag: well

value: endothelial

value: Late Car4- capillaries


title: S14 BRSV challenged

description: counts.txt


title: S13 BRSV challenged

description: counts.txt


title: Control_3

tag: strain

value: brain

tag: treatement

value: RU486 Drug Food

tag: age

value: Adult Day 8

tag: genotype


title: F_P7_normal_CD31_1_DC21_B18

tag: timepoint

tag: cell type

tag: cell subtype

value: Early Car4- capillaries

tag: mousename

tag: coverage

value: normal


title: S11 BRSV challenged

description: counts.txt

tag: breed

value: B


title: Gata3_Day4.6.pTEICM_6

tag: tissue

value: Blastoid

tag: lineage

value: Trophectoderm

tag: time point


title: Gata3_Day3.7.pTEICM_2

value: polar

value: 3 days after stem cells seeded to form cell aggregates


title: S8 BRSV challenged

description: counts.txt

value: BRSV challenged

value: Holstein-Friesian

tag: shed


title: F_P7_normal_CD31_1_DC21_F7

value: distal lung

tag: sequencing run

tag: gender

tag: plate

value: Proliferative EC

tag: number of genes


title: S9 BRSV challenged

description: counts.txt

tag: treatment


title: Gata3_Day4.5.pTEICM_16

value: 4 days after stem cells seeded to form cell aggregates


title: S6 control

description: counts.txt

value: control

value: A


title: S12 BRSV challenged

description: counts.txt


title: F_P7_normal_CD31_1_DC21_J13

value: F

tag: well

value: endothelial


title: F_P7_normal_CD31_1_DC21_J17


title: S7 BRSV challenged

description: counts.txt


title: F_P7_normal_CD31_1_DC21_E2


title: S2 control

description: counts.txt


title: S10 BRSV challenged

description: counts.txt


title: S5 control

description: counts.txt


title: S15 BRSV challenged

description: counts.txt

value: C


title: Gata3_Day4.5.pTEICM_15


title: Gata3_Day4.5.pTEICM_14


title: Gata3_Day4.5.pTEICM_13


title: S3 control

description: counts.txt


title: Gata3_Day4.5.pTEICM_18


title: S1 control

description: counts.txt


title: Gata3_Day4.5.pTEICM_17

value: Epiblast


title: Gata3_Day3.7.pTEICM_1


title: StAgo1-GFP 11388 3

extract_protocol:
Inoculated leaves were harvested and flash frozen in liquid nitrogen. StAGO1a-GFP co-IP were performed with anti-GFP antibody (Chromotek, gtm-100).
Barcoded sequencing libraries were constructed using the Ion Total RNA-Seq Kit v2 and Ion Xpress barcode primers. Sequencing was performed on the Ion Proton platform using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific).

tag: potato cultivar

value: StAgo1a-GFP (Sarpo Mira)

tag: p. infestans strain

tag: dpi

value: Infected leaves

tag: ip antibody

value: GFP (Chromotek, gtm-100)


title: F_P7_normal_CD31_1_DC21_H13

tag: timepoint

tag: cell type

tag: cell subtype

value: Late Car4- capillaries

tag: mousename

value: normal


title: StAgo1-GFP 11388 2

tag: tissue


title: Gata3_Day3.2.pTEICM_18

value: Blastoid

tag: lineage

value: Trophectoderm

value: polar

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_B19

value: distal lung

tag: sequencing run

value: Early Car4- capillaries

tag: coverage


title: StAgo1-GFP 11388 1


title: F_P7_normal_CD31_1_DC21_P9

tag: gender

tag: plate


title: S4 control

description: counts.txt

tag: treatment

value: control

tag: breed

value: Holstein-Friesian

tag: shed


title: StAgo1-GFP 88069 3

tag: potato cultivar

tag: p. infestans strain


title: Gata3_Day3.2.pTEICM_17


title: F_P7_normal_CD31_1_DC21_B9

value: F

tag: well

value: Arterial EC I

tag: number of genes


title: StAgo1-GFP 88069 1

tag: dpi

tag: ip antibody


title: Gata3_Day3.2.pTEICM_16


title: F_P7_normal_CD31_1_DC21_L23

tag: timepoint

tag: cell type

value: endothelial

tag: cell subtype

value: Proliferative EC

tag: mousename


title: Gata3_Day3.2.pTEICM_15

tag: tissue

tag: lineage

tag: time point


title: StAgo1-GFP 88069 2

value: StAgo1a-GFP (Sarpo Mira)


title: F_P7_normal_CD31_1_DC21_K6

tag: sequencing run

tag: gender

tag: plate

tag: coverage


title: Gata3_Day3.2.pTEICM_14


title: F_P7_normal_CD31_1_DC21_J9

value: Car4+ capillaries

tag: treatment


title: F_P21_normal_mesench_2_DC21_P17


title: CW2 Gal-9-Treated.Xenograft.tissue4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: microRNA

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: The human colon cancer cell lines CACO-2, CW-2, COLO-320, LoVo, and the colorectal cancer cell line WiDr were obtained from the Japanese Cancer Research Resources Bank (Tokyo, Japan). All the cell lines were certified by STRA and mycoplasma testing has been done for cell lines used in our experiments. The cells were cultured in RPMI-1640 (Gibco Invitrogen, Carlsbad, CA, USA) supplemented with 10% heat-inactivated FBS, and penicillin-streptomycin (100 μg/ml; Invitrogen) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: After incubation for 24 h, cells were treated with 0.01, 0.03, 0.1, and 0.3 μM of Gal-9 added to the culture medium and subsequently cultured for an additional 48 h.

tag: sample type

value: Colon cancer cell xenograft tumor

value: 90 ug galectin-9


title: CW2 Gal-9-Treated.Xenograft.tissue3

description: microRNA


title: CW2 Control.Xenograft.tissue3

description: microRNA


title: CW2 Control.Xenograft.tissue4

description: microRNA


title: CW2 Gal-9-Treated.Xenograft.tissue2

description: microRNA


title: CW2 Gal-9-Treated.Xenograft.tissue1

description: microRNA


title: Day6.2.mTE_4

source_name: Blastocyst

value: Blastocyst

value: mural

value: Embryonic day 6


title: Gata3_Day4.5.pTEICM_12

value: Blastoid

value: Trophectoderm

value: polar

value: 4 days after stem cells seeded to form cell aggregates


title: CW2 Control.Xenograft.tissue2

description: microRNA

value: control


title: RNAseq_si_hnRNPK_rep3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trim_galore 0.6.6.
The filtered reads were mapped to the hg38 genome using STAR.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by featureCounts.
Differentially expressed merged transcripts were quantified using EdgeR.
Genome_build: hg38
Supplementary_files_format_and_content: xls files include RPKM values for each Sample.

source_name: NCI-H1299 total RNA

growth_protocol: Colonial cultures were maintained in the 1640 medium

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

treatment_protocol: BEAS-2B and NCI-H1299 were treated with DMSO and TSA respectively for 24 hours to produce 10 samples, and NCI-H1299 was treated with RNA oligo to produce 12 samples.

value: si-hnRNP K


title: RNAseq_si_hnRNPK_rep2


title: Gata3_Day4.5.pTEICM_11

source_name: Blastoid

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen.
The Smart-Seq2 library was prepared as described in Picelli S et al. 2014.


title: F_P21_normal_mesench_1_DC21_K1

source_name: distal lung

extract_protocol:
no extraction
scRNA-Seq: plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

value: distal lung

value: F

tag: well

value: Late Car4- capillaries

value: normal


title: Gata3_Day4.5.pTEICM_10


title: RNAseq_si_hnRNPK_rep1


title: F_P7_normal_CD31_1_DC21_O21

value: endothelial

value: Proliferative EC

tag: number of genes


title: RNAseq_hnRNPK_NC_rep3

value: si-NC


title: RNAseq_hnRNPK_NC_rep2


title: RNAseq_hnRNPK_NC_rep1


title: Gata3_Day4.5.pTEICM_9


title: RNAseq_sh_LCDR_rep3

value: sh-LCDR


title: RNAseq_sh_LCDR_rep2


title: F_P7_normal_CD31_1_DC21_P5

value: Lymphatic EC


title: F_P7_normal_CD31_1_DC21_H18

value: Early Car4- capillaries


title: RNAseq_sh-Con_rep3

value: sh-Con


title: Gata3_Day4.5.pTEICM_7

value: Blastoid


title: RNAseq_sh-Con_rep1


title: F_P7_normal_CD31_1_DC21_O14

value: Car4+ capillaries


title: RNAseq_sh-Con_rep2


title: RNAseq_NCI_H1299_TSA_rep2

description: RNAseq_NCI_H1299_DMSO-TSA_all_gene_RPKM.xls

value: TSA


title: RNAseq_NCI_H1299_TSA_rep1


title: CW2 Control.Xenograft.tissue1

description: microRNA

value: Colon cancer cell xenograft tumor


title: F_P21_normal_mesench_2_DC21_A15


title: Gata3_Day4.5.pTEICM_6

value: Trophectoderm

value: polar

value: 4 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_P16

value: distal lung

value: F

value: Venous EC


title: F_P7_normal_CD31_1_DC21_O11

value: endothelial

value: normal


title: RNAseq_NCI_H1299_DMSO_rep1

value: DMSO


title: Day6.2.mTE_2

value: Blastocyst

value: mural

value: Embryonic day 6


title: Gata3_Day4.5.pTEICM_5


title: F_P7_normal_CD31_1_DC21_D9

value: Late Car4- capillaries


title: F_P7_normal_CD31_1_DC21_D5


title: RNAseq_BEAS_2B_TSA_rep3

description: RNAseq_BEAS_2B_DMSO-TSA_all_gene_RPKM.xls

source_name: BEAS-2B total RNA


title: RNAseq_BEAS_2B_TSA_rep1


title: Day6.2.pTEICM_30


title: F_P7_normal_CD31_1_DC21_K12

value: Early Car4- capillaries


title: RNAseq_BEAS_2B_DMSO_rep3


title: Gata3_Day4.5.pTEICM_8

value: Blastoid


title: RNAseq_BEAS_2B_TSA_rep2

value: TSA


title: Day6.2.pTEICM_29


title: RNAseq_sh_LCDR_rep1

value: sh-LCDR


title: F_P7_normal_CD31_1_DC21_P15


title: RNAseq_BEAS_2B_DMSO_rep1


title: Day6.2.pTEICM_27

value: Trophectoderm


title: F_P21_normal_mesench_2_DC21_K5


title: Day6.2.pTEICM_26

value: Epiblast

value: polar


title: F_P21_normal_mesench_2_DC21_B12

value: distal lung


title: RNAseq_NCI_H1299_DMSO_rep2


title: paracancerous tissue 2

city: Shanghai

first: Yiqun

last: Yu

address: 83 Fengyang Road, Xuhui

department: Otolaryngology

institute: Eye, Ear, Nose and Throat Hospital, Fudan University

description: LB-QM-0245-18__2_FKDL190737454-1a-4_HWG53CCXY_L5_1

data_processing:
Sequencing reads were mapped to the human genome using HISAT2.
Transcriptome from RNA-seq reads was reconstructed byStringTie
Expression differences were evaluated using DESeq2.
Genome_build: gencode v27
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: paracancerous tissue

extract_protocol:
Total RNA was extracted by using E.Z.N.A.® Total RNA Kit I (Omega, R6834-02) according to the manufacturer’s manual.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: paracancerous tissue 1

description: LB-QM-0245-7__2_FKDL190737454-1a-2_HWG53CCXY_L5_1


title: paracancerous tissue 3

description: LB-QM-0245-28__2_FKDL190737454-1a-6_HWG53CCXY_L5_1


title: F_P7_normal_CD31_1_DC21_N23

value: F

value: Arterial EC I


title: nasopharyngeal carcinoma 3

description: LB-QM-0245-28__1_FKDL190737454-1a-5_HWG53CCXY_L5_1

source_name: nasopharyngeal carcinoma tisssue

value: tumor


title: nasopharyngeal carcinoma 1

description: LB-QM-0245-7__1_FKDL190737454-1a-1_HWG53CCXY_L5_1


title: nasopharyngeal carcinoma 2

description: LB-QM-0245-18__1_FKDL190737454-1a-3_HWG53CCXY_L5-1


title: Gata3_Day4.5.pTEICM_4

value: 4 days after stem cells seeded to form cell aggregates


title: Gata3_Day4.5.pTEICM_3


title: F_P7_normal_CD31_1_DC21_J15

value: endothelial

value: normal


title: Gata3_Day4.5.pTEICM_2


title: Gata3_Day4.5.pTEICM_1


title: RNAseq_BEAS_2B_DMSO_rep2

value: DMSO


title: F_P7_normal_CD31_1_DC21_F5


title: Gata3_Day4.1.pTEICM_43


title: F_P7_normal_CD31_1_DC21_C14

value: Proliferative EC


title: Gata3_Day4.1.pTEICM_42


title: F_P7_normal_CD31_1_DC21_G22


title: F_P21_normal_mesench_1_DC21_N17

value: Late Car4- capillaries


title: Gata3_Day4.1.pTEICM_41


title: Gata3_Day4.1.pTEICM_40

value: Primitive Endoderm


title: F_P7_normal_CD31_1_DC21_N5

value: Early Car4- capillaries


title: Day6.2.pTEICM_24

value: Blastocyst

value: Embryonic day 6


title: F_P7_normal_CD31_1_DC21_N22


title: F_P7_normal_CD31_1_DC21_I21


title: LPS+TMT Replicate Replicate 1

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression data

hyb_protocol: Amplified biotin-cDNAs (5.5μg) were fragmented and hybridized for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification (GeneChip Hybridization, Wash and Stain Kit).

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using Transcriptome Analysis Console 4.0 Software.

data_processing: Array data were pre-processing and normalized by the affy package.  The Robust Multichip Analysis (RMA) approach was applied for the normalization.

label: biotin

source_name: Murine bone marrow derived macrophages

label_protocol: Gene expression analysis was conducted on 3 biological replicates using Affymetrix Mouse Genome 430 2.0 GeneChip® arrays (Affymetrix).  Total RNA (50ng) was amplified as directed in the Nugen WT-Ovation Pico RNA Amplification System protocol and labeling with biotin following the Nugen Encore Biotin Module protocol.

growth_protocol: C57BL6 mice (6-12-weeks-old) were euthanized under CO2, the femur excised, bone marrow extruded, and primary BMDMs cultured. Isolated cells were plated 1,000,000 cells/well/12-well plate in 3 mL DMEM supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 10% L929 conditioned-media.  On days-in-vitro (DIV)4, cells underwent a half-media change.  On DIV5, media was changed to DMEM without L929 conditioned medium.  Cells were used in experiments on DIV6.

extract_protocol: Total RNA was isolated from BMDMs using TRIzol® (Invitrogen).  Resuspended pellets were treated with 2.5L DNase I and 10L Buffer RDD for 10 min at RT followed by column separation (RNeasy mini prep, Qiagen).

treatment_protocol: On DIV6, cells were treated with 33 ng/mL ultrapure LPS for 3 hours prior to the addition of either TMT OH (1.25M), TET Br (10M), or sterile saline for 6 hours.

tag: strain

value: bone marrow derived macrophages

value: LPS prime+TMT


title: Day6.2.pTEICM_19

value: Trophectoderm

value: polar


title: F_P7_normal_CD31_1_DC21_P17

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

value: distal lung

value: F

value: Car4+ capillaries


title: LPS+TET Replicate Replicate 2

description: Gene expression data

value: LPS prime+TET


title: LPS Replicate Replicate 1

description: Gene expression data

value: LPS prime


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description: Biological replicate 6 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: U87 human Glioblastoma multiforme cell line

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. U87 GBM cells exposed to acute hypoxia were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA of the chosen control, was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: U87 GBM cell line exposed to PT during hypoxia, were collected after 24 hours post treatments.

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

value: Glioblastoma cell line

tag: cell line

value: exposed to acute hypoxia


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 2

description: Biological replicate 2 of 6


title: LPS Replicate Replicate 3

description: Gene expression data


title: LPS+TMT Replicate Replicate 2

description: Gene expression data


title: LPS+TMT Replicate Replicate 3

description: Gene expression data


title: LPS+TET Replicate Replicate 1

description: Gene expression data


title: Day6.2.pTEICM_17

data_processing:
Trim-Galore
STAR
FeatureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts_raw.txt: Raw counts text file.


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 3

description: Biological replicate 3 of 6


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 4

description: Biological replicate 4 of 6


title: LPS+TET Replicate Replicate 3

description: Gene expression data


title: LPS Replicate Replicate 2

description: Gene expression data


title: F_P7_normal_CD31_1_DC21_C5

first: Fabio

last: Zanini

institute: University of New South Wales

tag: timepoint

value: endothelial

value: normal


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 1

description: Biological replicate 1 of 6

tag: cell type


title: F_P7_normal_CD31_1_DC21_A9

tag: cell subtype

value: Late Car4- capillaries


title: Gata3_Day4.1.pTEICM_38

first: Daniel

last: Spindlow

institute: University of Exeter

value: Blastoid

value: 4 days after stem cells seeded to form cell aggregates


title: Gata3_Day4.1.pTEICM_39

value: Epiblast


title: 20-SR-PFR5-28h

city: Stuttgart

first: Julia

last: Zieringer

department: Biochemical Engineering

country: Germany

institute: University of Stuttgart

description: Escherichia coli SR

data_processing:
Trimmomatic v. 0.32 (Bolger et al., 2014) was used to remove adapters and low quality reads (<Q20) checked by fastqc reports. Genes were aligned to the NCBI E. coli K12 MG1655 reference genome (RefSeq: NC_000913.3) using the RNA-sequencing aligner Bowtie2 v. 2.3.2.2 (Langmead and Salzberg, 2012). Aligned reads were counted for each gene based on the corresponding annotation available from NCBI for the chosen reference sequence applying HTseq-count v. 0.6.1 (Anders et al., 2014) in the union mode.
Differential gene expression analysis was performed with the R-package DeSeq2 v. 1.26.0 (Love et al., 2014) available from Bioconductor (Gentleman et al., 2004) (http://www.bioconductor.org). Prior to statistical analysis, all residual non-protein encoding RNA molecules (tRNA, rRNA and sRNA) were removed from the HTseq-derived raw count data and a non-speciﬁc ﬁlter was applied to remove low coverage genes with fewer than two counts per million (54 reads on average). All filtering steps caused deviations from the raw data of less than 6 %. Samples were grouped by replicates and an experimental design was chosen that used sample time and location (STR or PFR) as a combined environmental factor. To normalize the read counts for comparison purposes on sequencing depth and RNA composition, DESeq2 uses the median of ratios method to derive a scaling factor.. Resulting p-values were adjusted for multiple testing according to Benjamini and Hochberg (1995) to control the false discovery rate (FDR). Genes were identiﬁed as signiﬁcantly diﬀerentially expressed by applying FDR adjusted p-values < 0.01 and a log2 fold change ≥ |1|.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: xlsx file formate includes raw gene counts for each sample before and after filtering for low coverage genes. Additionally normalized gene counts are included.

organism: Escherichia coli

growth_protocol: A small amount of glycerol stock seed culture was spread onto 2xYT agar plates and incubated at 37 °C for 24 h. A single colony was picked to inoculate 500 ml baffled shaking flasks with 50 ml of preculture minimal media. Flasks were then incubated at 37 °C on an orbital shaker set to 150 rpm for 16 hours. In the next morning 500 µl of biosuspension were transferred to 1000 ml baffled shaking flasks containing 100 ml preculture minimal media and incubated at 37 °C on an orbital shaker set to 150 rpm for 8 hours. 50 ml of this culture were used to inoculate the bioreactor. Total volume in the bioreactor was 1.6 l after inoculation. Batch fermentation in the bioreactor ensued at 28-30 °C overnight. In the next morning feed and harvest trains were connected and a constant feed/harvest rate at 5.33 ml/min corresponding to a dilution rate of 0.2 h-1 established. After 25 h (five residence times) a reference sample was taken (t0). The plug-flow reactor was then connected to the primary reactor via a diaphragm metering pump effectively circulating about one-quarter of the total fermentation broth from the primary reactor through the plug-flow reactor and back into the stirred tank reactor. In the following 28 h samples were taken at predefined time points from the STR and the five PFR ports. After these 28 h the fermentation was aborted, and the final broth volume measured.

extract_protocol:
0.5 ml broth was sampled from the bioreactor and directly flash-frozen in liquid nitrogen. Frozen broth was then stored at -70 °C until the day of RNA isolation. Total RNA was isolated using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Isolated RNA was DNAse treated and shipped to commercial sequencing partner GENEWIZ® on dry ice. Samples were treated for rRNA depletion, sequencing libraries prepared and Illumina HiSeq 2x150 bp sequencing performed. Raw FASTQ files were obtained for bioinformatic analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SR

tag: replicates

value: J

tag: condition

value: nlim-nstarv

tag: sample port


title: U87 GBM cell line treated with 10 Gy of proton dose during acute hypoxia - replicate 5

description: Biological replicate 5 of 6


title: F_P21_normal_mesench_1_DC21_J19

city: Kensington

tag: tissue

tag: mousename


title: 18-SR-PFR5-5min

description: Escherichia coli SR

tag: time point

value: H


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 4

description: Biological replicate 4 of 6


title: F_P7_normal_CD31_1_DC21_N6

value: distal lung

tag: sequencing run

tag: gender

tag: plate


title: 17-SR-STR-5min

description: Escherichia coli SR

value: G

value: S


title: Gata3_Day4.1.pTEICM_37

city: Exeter

tag: lineage

value: Trophectoderm

value: polar


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 3

description: Biological replicate 3 of 6

value: Glioblastoma cell line

tag: treatment


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 5

description: Biological replicate 5 of 6

value: exposed to acute hypoxia


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 6

description: Biological replicate 6 of 6


title: 16-SR-STR-0h

description: Escherichia coli SR

value: F


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 1

description: Biological replicate 1 of 6


title: Gata3_Day4.1.pTEICM_36


title: 15-WT-PFR5-28h

description: Escherichia coli WT MG1665

value: E


title: F_P7_normal_CD31_1_DC21_F22

tag: well

value: endothelial

value: Early Car4- capillaries

tag: coverage

tag: number of genes

value: normal


title: 14-WT-STR-28h

description: Escherichia coli WT MG1665

tag: strain

value: D


title: 11-WT-STR-0h

description: Escherichia coli WT MG1665

value: A


title: 12-WT-STR-5min

description: Escherichia coli WT MG1665

value: B


title: 19-SR-STR-28h

description: Escherichia coli SR

value: SR

value: I

value: nlim-nstarv


title: Gata3_Day4.1.pTEICM_34

value: Blastoid

value: 4 days after stem cells seeded to form cell aggregates


title: 13-WT-PFR5-5min

description: Escherichia coli WT MG1665

value: C


title: F_P7_normal_CD31_1_DC21_D15

value: distal lung

tag: timepoint

tag: cell type

value: Car4+ capillaries


title: Gata3_Day4.1.pTEICM_35

value: Trophectoderm

value: polar


title: F_P7_normal_CD31_1_DC21_I9

value: F

tag: cell subtype

value: Proliferative EC


title: Gata3_Day4.1.pTEICM_32


title: 9-SR-STR-28h

description: Escherichia coli SR

tag: replicates

tag: condition

value: S


title: Gata3_Day4.1.pTEICM_33

tag: tissue


title: 8-SR-PFR5-5min

description: Escherichia coli SR

value: H

tag: sample port


title: 10-SR-PFR5-28h

description: Escherichia coli SR

tag: time point

value: J


title: 7-SR-STR-5min

description: Escherichia coli SR

value: G


title: F_P7_normal_CD31_1_DC21_L11

tag: sequencing run

value: endothelial

tag: mousename

value: normal


title: 5-WT-PFR5-28h

description: Escherichia coli WT MG1655

value: E


title: F_P21_normal_mesench_1_DC21_M5

tag: gender

tag: plate


title: 6-SR-STR-0h

description: Escherichia coli SR

value: SR

value: nlim-nstarv


title: Day6.2.pTEICM_14

value: Blastocyst

tag: lineage

value: Embryonic day 6


title: Day6.2.pTEICM_12


title: F_P7_normal_CD31_1_DC21_G21

value: distal lung

tag: well

value: Early Car4- capillaries

tag: treatment


title: 3-WT-PFR5-5min

description: Escherichia coli WT MG1655

value: C


title: 2-WT-STR-5min

description: Escherichia coli WT MG1655

value: B


title: Day6.2.pTEICM_11

value: Epiblast

value: polar


title: 1-WT-STR-0h

description: Escherichia coli WT MG1655

value: A

value: S


title: A549 cell line si-CBX3 #3

city: Wuhan

first: Haixin

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using Hisat2 v2.0.5
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read-counts and FPKM values for each Sample.

source_name: A549 cells

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First   Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: 4-WT-STR-28h

description: Escherichia coli WT MG1655

value: D


title: F_P21_normal_mesench_1_DC21_F2

address: High and Botany St

value: F

value: Late Car4- capillaries

tag: coverage

tag: number of genes


title: A549 cell line si-CBX3 #1


title: Gata3_Day4.1.pTEICM_31

address: Stocker Road

value: Blastoid

value: 4 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_B13

tag: timepoint

value: endothelial

value: normal


title: F_P21_normal_mesench_2_DC21_B15

tag: cell type


title: A549 cell line si-Control #2

value: si-Control


title: Gata3_Day4.1.pTEICM_30

value: Trophectoderm


title: F_P21_normal_mesench_2_DC21_I8

value: distal lung

tag: cell subtype

value: Car4+ capillaries


title: A549 cell line si-Control #1


title: Normal brain tissue-3

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
Normal Brain Tissue
NB3

data_processing:
Paired-end reads were aligned using STAR 2.5.3a and quantified using RSEM v1.3 with Gencode v24 annotation.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM gene expression values

source_name: Brain Tissue

extract_protocol:
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol

value: brain

tag: disease state

value: Normal

tag: patient id

tag: molecular subtype


title: Normal brain tissue-2

description:
Normal Brain Tissue
NB2

tag: tissue


title: Day6.2.pTEICM_10

value: Blastocyst

value: Epiblast

tag: time point

value: Embryonic day 6


title: F_P7_normal_CD31_1_DC21_H22

tag: sequencing run


title: Normal brain tissue-1

description:
Normal Brain Tissue
NB1


title: F_P21_normal_mesench_2_DC21_K14

tag: mousename


title: Primary GBM SuR38

description:
Primary GBM
GBM38

value: Glioblastoma

value: Proneural


title: Primary GBM SuR37

description:
Primary GBM
GBM37

value: Mesenchymal


title: Gata3_Day4.1.pTEICM_28

value: polar


title: Primary GBM SuR36

description:
Primary GBM
GBM36


title: Gata3_Day4.1.pTEICM_27

value: Blastoid


title: F_P21_normal_mesench_2_DC21_P1

tag: gender

value: F

value: Late Car4- capillaries


title: Primary GBM SuR35

description:
Primary GBM
GBM35


title: A549 cell line si-CBX3 #2


title: Gata3_Day4.1.pTEICM_26

value: 4 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_I17

tag: plate

value: endothelial

value: Venous EC

value: normal


title: Primary GBM SuR34

description:
Primary GBM
GBM34


title: A549 cell line si-Control #3

value: si-Control


title: Primary GBM SuR33

description:
Primary GBM
GBM33

value: brain


title: Primary GBM SuR32

description:
Primary GBM
GBM32

value: Classical


title: F_P7_normal_CD31_1_DC21_E13

value: distal lung


title: F_P7_normal_CD31_1_DC21_C7

value: Proliferative EC


title: Primary GBM SuR29

description:
Primary GBM
GBM29


title: Primary GBM SuR30

description:
Primary GBM
GBM30


title: Primary GBM SuR31

description:
Primary GBM
GBM31


title: Gata3_Day4.1.pTEICM_23

tag: lineage

value: Trophectoderm


title: Gata3_Day4.1.pTEICM_22


title: Primary GBM SuR28

description:
Primary GBM
GBM28

value: Glioblastoma


title: Primary GBM SuR27

description:
Primary GBM
GBM27


title: Primary GBM SuR26

description:
Primary GBM
GBM26


title: F_P7_normal_CD31_1_DC21_A1

tag: well

value: Car4+ capillaries


title: Gata3_Day4.1.pTEICM_21


title: Primary GBM SuR24

description:
Primary GBM
GBM24

value: Proneural


title: Gata3_Day4.1.pTEICM_20

value: polar


title: Primary GBM SuR25

description:
Primary GBM
GBM25

value: Mesenchymal


title: Primary GBM SuR22

description:
Primary GBM
GBM22


title: F_P7_normal_CD31_1_DC21_A4

value: F

tag: treatment


title: Primary GBM SuR21

description:
Primary GBM
GBM21


title: Gata3_Day4.1.pTEICM_19

value: Blastoid


title: F_P7_normal_CD31_1_DC21_G18

value: Early Car4- capillaries

tag: coverage


title: Gata3_Day4.1.pTEICM_25

value: Primitive Endoderm

value: 4 days after stem cells seeded to form cell aggregates


title: Gata3_Day4.1.pTEICM_18


title: F_P21_normal_mesench_2_DC21_I6

value: endothelial

value: Late Car4- capillaries

tag: number of genes

value: normal


title: Primary GBM SuR17

description:
Primary GBM
GBM17

value: brain


title: Primary GBM SuR18

description:
Primary GBM
GBM18


title: Primary GBM SuR15

description:
Primary GBM
GBM15


title: F_P7_normal_CD31_1_DC21_C21

value: distal lung

tag: timepoint


title: Gata3_Day3.3.pTEICM_40

value: Epiblast

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_B20

tag: cell type


title: F_P7_normal_CD31_1_DC21_E12

tag: cell subtype

value: Proliferative EC


title: Primary GBM SuR14

description:
Primary GBM
GBM14

tag: disease state

value: Glioblastoma


title: Primary GBM SuR12

description:
Primary GBM
GBM12

tag: patient id

value: Classical


title: Gata3_Day3.3.pTEICM_39

value: Trophectoderm

value: polar


title: Primary GBM SuR13

description:
Primary GBM
GBM13

tag: molecular subtype


title: F_P7_normal_CD31_1_DC21_O5

tag: tissue

value: F


title: F_P7_normal_CD31_1_DC21_I7


title: Primary GBM SuR09

description:
Primary GBM
GBM09


title: Primary GBM SuR10

description:
Primary GBM
GBM10

value: Proneural


title: Gata3_Day3.3.pTEICM_38

value: Blastoid

tag: time point


title: Primary GBM SuR11

description:
Primary GBM
GBM11


title: Gata3_Day3.3.pTEICM_37


title: F_P7_normal_CD31_1_DC21_D11

tag: sequencing run


title: Primary GBM SuR16

description:
Primary GBM
GBM16


title: Gata3_Day4.1.pTEICM_17


title: Primary GBM SuR02

description:
Primary GBM
GBM02

value: Mesenchymal


title: Gata3_Day3.3.pTEICM_36


title: Primary GBM SuR03

description:
Primary GBM
GBM03


title: F_P7_normal_CD31_1_DC21_J11

tag: mousename


title: Primary GBM SuR01

description:
Primary GBM
GBM01


title: U343-input

description: GBM  ChIP-seq Input

library_source: genomic

data_processing:
Raw fastq files were aligned to human gneome using bwa v0.7.12 to human genome hg38. Peaks were called using MACS2 v2.1.0.20150731 with parameters -g hs --keep-dup all -B --SPMR --nomodel --extsize 200 -q 0.01. The bedgraph file was later converted using UCSC bedGraphToBigWig utility.
Genome_build: hg38
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million.

molecule: genomic DNA

source_name: GBM cell line with ChIP-seq input

extract_protocol:
ChIP was performed by following a standard protocol. Briefly, cells were dissociated and fixed with 1% formaldehyde for 10 min at room temperature, followed with 3 washes by cold PBS. Nuclei were extracted and re-suspended in SDS lysis buffer for 10 min on ice before sonication by Bioruptor (Diagenode). Optimal condition of sonication yielded genomic fragments around 200 to 500 bp. After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min). Supernatant was then pre-cleared and incubated with magnetic beads (Invitrogen Dynabeads) conjugated with specific antibodies against H3K27ac (Activemotif, #39133).  After overnight incubation, magnetic beads were washed stepwise with cold low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. Bound DNA was eluted, reverse-crosslinked, and purified by QIAquick PCR purification kit (Qiagen).
Standard Illumina library preparation protocol

value: GBM cell line

tag: chip antibody


title: Primary GBM SuR05

description:
Primary GBM
GBM05


title: Gata3_Day3.3.pTEICM_35


title: Gata3_Day3.3.pTEICM_34


title: F_P7_normal_CD31_1_DC21_M11

tag: gender

tag: plate

value: endothelial


title: F_P7_normal_CD31_1_DC21_M6

tag: well

value: Early Car4- capillaries


title: Gata3_Day3.3.pTEICM_33

tag: lineage


title: Primary GBM SuR07

description:
Primary GBM
GBM07


title: U251-H3k27ac

description: GBM  H3K27ac ChIP-seq

source_name: GBM cell line with H3K27ac ChIP-seq

value: H3K27ac (Activemotif, #39133)


title: U343-H3k27ac

description: GBM  H3K27ac ChIP-seq


title: NNI31-input

description: GBM  ChIP-seq Input

source_name: GBM propagating cells with ChIP-seq input


title: F_P7_normal_CD31_1_DC21_M23

tag: coverage

tag: treatment

value: normal


title: NNI31-H3k27ac

description: GBM  H3K27ac ChIP-seq

source_name: GBM propagating cells with H3K27ac ChIP-seq


title: F_P21_normal_mesench_1_DC21_L16

value: distal lung

tag: timepoint

value: Late Car4- capillaries

tag: number of genes


title: NNI24-input

description: GBM  ChIP-seq Input


title: Gata3_Day4.1.pTEICM_15

value: 4 days after stem cells seeded to form cell aggregates


title: NNI24-H3k27ac

description: GBM  H3K27ac ChIP-seq


title: F_P7_normal_CD31_1_DC21_E22

tag: cell type

tag: cell subtype


title: NNI23-input

description: GBM  ChIP-seq Input

tag: patient id


title: F_P7_normal_CD31_1_DC21_I14


title: NNI11-input

description: GBM  ChIP-seq Input


title: NNI23-H3k27ac

description: GBM  H3K27ac ChIP-seq


title: F_P7_normal_CD31_1_DC21_P7

value: Car4+ capillaries


title: Gata3_Day4.1.pTEICM_12


title: Gata3_Day4.1.pTEICM_11


title: F_P7_normal_CD31_1_DC21_K9


title: NNI11-H3k27ac

description: GBM  H3K27ac ChIP-seq


title: DBTRG-input

description: GBM  ChIP-seq Input

value: DBTRG


title: DBTRG-H3k27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day4.1.pTEICM_9


title: U87 GBM cell line treated with 2 Gy of proton dose during acute hypoxia - replicate 2

description: Biological replicate 2 of 6

value: Glioblastoma cell line

tag: cell line

value: exposed to acute hypoxia


title: NB3_input

description: Normal  ChIP-seq Input

source_name: Normal brain tissue with ChIP-seq input

tag: tissue

value: normal brain tissue


title: Gata3_Day4.1.pTEICM_10

value: Trophectoderm

value: polar

tag: time point


title: F_P7_normal_CD31_1_DC21_E19

tag: sequencing run

value: F

value: Arterial EC I


title: F_P7_normal_CD31_1_DC21_I12

value: Proliferative EC

tag: mousename


title: NB3_H3K27ac

description: Normal  H3K27ac ChIP-seq

source_name: Normal brain tissue with H3K27ac ChIP-seq

tag: chip antibody


title: NB2_input

description: Normal  ChIP-seq Input


title: NB2_H3K27ac

description: Normal  H3K27ac ChIP-seq


title: Gata3_Day4.1.pTEICM_13

value: Blastoid


title: NB1_input

description: Normal  ChIP-seq Input


title: Gata3_Day4.1.pTEICM_8


title: Gata3_Day3.3.pTEICM_32

value: Epiblast

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_D8

tag: gender

value: endothelial

value: normal


title: F_P7_normal_CD31_1_DC21_C6

value: distal lung

tag: plate


title: GBM38_H3K27ac

description: GBM  H3K27ac ChIP-seq

source_name: GBM sample with H3K27ac ChIP-seq

value: GBM tissue

value: H3K27ac (Activemotif, #39133)


title: Gata3_Day3.3.pTEICM_31


title: Gata3_Day3.3.pTEICM_30


title: GBM36_input

description: GBM  ChIP-seq Input

source_name: GBM sample with ChIP-seq input


title: GBM37_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: F_P7_normal_CD31_1_DC21_C18

tag: well

value: Late Car4- capillaries


title: GBM36_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_29

source_name: Blastoid

tag: lineage


title: GBM37_input

description: GBM  ChIP-seq Input


title: GBM34_input

description: GBM  ChIP-seq Input


title: Gata3_Day3.3.pTEICM_28


title: F_P7_normal_CD31_1_DC21_L6

source_name: distal lung

tag: coverage


title: GBM33_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_M14

value: Car4+ capillaries

tag: treatment


title: F_P7_normal_CD31_1_DC21_J10

tag: timepoint

value: Early Car4- capillaries


title: NB1_H3K27ac

description: Normal  H3K27ac ChIP-seq

value: normal brain tissue


title: Gata3_Day3.3.pTEICM_27


title: GBM38_input

description: GBM  ChIP-seq Input


title: GBM34_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM33_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_26

value: Trophectoderm


title: F_P7_normal_CD31_1_DC21_L19

tag: number of genes


title: GBM32_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day4.1.pTEICM_7

value: polar

value: 4 days after stem cells seeded to form cell aggregates


title: GBM31_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_E18

value: F

tag: cell type

value: Venous EC


title: GBM35_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_C16

tag: cell subtype


title: GBM35_H3K27ac

description: GBM  H3K27ac ChIP-seq

tag: patient id


title: Gata3_Day4.1.pTEICM_29

value: Blastoid


title: GBM30_input

description: GBM  ChIP-seq Input


title: Gata3_Day4.1.pTEICM_5


title: GBM30_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM29_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_M22


title: GBM29_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM32_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_C1


title: F_P21_normal_mesench_1_DC21_G1


title: Gata3_Day4.1.pTEICM_3


title: Gata3_Day4.1.pTEICM_2


title: GBM28_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day4.1.pTEICM_1


title: GBM27_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM26_input

description: GBM  ChIP-seq Input


title: GBM27_input

description: GBM  ChIP-seq Input


title: GBM26_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_24


title: F_P7_normal_CD31_1_DC21_J8


title: GBM31_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM25_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day4.1.pTEICM_4


title: F_P7_normal_CD31_1_DC21_G13

value: Proliferative EC


title: GBM24_input

description: GBM  ChIP-seq Input


title: Gata3_Day3.3.pTEICM_22

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_A6

value: endothelial


title: GBM22_input

description: GBM  ChIP-seq Input


title: GBM28_input

description: GBM  ChIP-seq Input


title: GBM22_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM24_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM21_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_L2

value: normal


title: F_P7_normal_CD31_1_DC21_J18

value: distal lung


title: F_P7_normal_CD31_1_DC21_L21


title: Gata3_Day3.3.pTEICM_20

value: Epiblast


title: F_P7_normal_CD31_1_DC21_M19


title: GBM21_H3K27ac

description: GBM  H3K27ac ChIP-seq

value: GBM tissue

value: H3K27ac (Activemotif, #39133)


title: Gata3_Day3.3.pTEICM_19


title: GBM18_input

description: GBM  ChIP-seq Input


title: GBM18_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_18


title: Gata3_Day3.3.pTEICM_21


title: Gata3_Day3.3.pTEICM_23


title: F_P7_normal_CD31_1_DC21_E8

value: Late Car4- capillaries


title: GBM25_input

description: GBM  ChIP-seq Input


title: GBM17_input

description: GBM  ChIP-seq Input


title: Muscle_Old SX_biological rep7

city: Saint Genes Champanelle

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

hyb_protocol: Following fragmentation and terminal labeling, 5.5 µg of single stranded cDNA were hybridized for 16 h at 45°C and 60 rpm on GeneChip® Human Exon 1.0 ST Array in the Affymetrix Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization Wash and Stain Affymetrix kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were generated with Affymetrix Expression Console v 1.2.1 software using robust multiarray average (RMA) algorithm. Affymetrix data files were processed using GeneSpring GX 14.9 13 (Agilent ).

source_name: vastus lateralis, old SX

label_protocol: Biotinylated single stranded cDNA were prepared from 400 ng of depleted total RNA according to the Affymetrix WT protocol (Ambion WT Expression kit).

growth_protocol: Vastus lateralis muscle biopsy from men

extract_protocol: Vastus lateralis biopsies were snap-frozen in liquid N2. RNA was isolated using a TissueRuptor and RNeasy Fibrous Tissue Mini Kit (Qiagen). Integrity of RNA  was verified using an Agilent Bioanalyser with the RNA 6000 Nano labchip® kit (Agilent). Concentration and purity was determined with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies). The depletion of the ribosomal fractions was processed using 2 µg of total RNA and magnetic beads from Ribominus Kit (Invitrogen).

value: male

tag: age (y)

tag: disease state

value: metabolic syndrome

value: vastus lateralis muscle


title: F_P7_normal_CD31_1_DC21_P2

tag: tissue

value: Early Car4- capillaries


title: GBM17_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_16

value: polar

tag: time point


title: Muscle_Old SX_biological rep6


title: GBM16_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_F9

tag: sequencing run

value: F

tag: mousename


title: Gata3_Day3.3.pTEICM_17


title: F_P7_normal_CD31_1_DC21_I20

tag: gender


title: Muscle_Old SX_biological rep5


title: F_P7_normal_CD31_1_DC21_B4

tag: plate


title: GBM16_H3K27ac

description: GBM  H3K27ac ChIP-seq

tag: chip antibody


title: Gata3_Day3.3.pTEICM_14

tag: lineage

value: Trophectoderm


title: F_P21_normal_mesench_1_DC21_H1

tag: well

tag: coverage


title: Gata3_Day3.3.pTEICM_12

value: Blastoid


title: GBM15_input

description: GBM  ChIP-seq Input


title: Muscle_Old SX_biological rep4


title: Gata3_Day3.3.pTEICM_11


title: GBM15_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: F_P7_normal_CD31_1_DC21_G2

tag: timepoint

tag: treatment


title: Muscle_Old SX_biological rep2


title: GBM14_input

description: GBM  ChIP-seq Input


title: Muscle_Old SX_biological rep3


title: Gata3_Day3.3.pTEICM_10


title: Gata3_Day3.3.pTEICM_15


title: F_P7_normal_CD31_1_DC21_B5

tag: cell type

value: Car4+ capillaries

tag: number of genes


title: U251-input

description: GBM  ChIP-seq Input

value: GBM cell line

tag: patient id


title: GBM14_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Muscle_Old_biological rep12

source_name: vastus lateralis, old

tag: age (y)

value: healthy


title: Gata3_Day3.3.pTEICM_9

value: 3 days after stem cells seeded to form cell aggregates


title: Muscle_Old SX_biological rep1

tag: disease state


title: Muscle_Old_biological rep11

tag: tissue


title: F_P7_normal_CD31_1_DC21_P21

value: distal lung

value: endothelial

tag: cell subtype

value: normal


title: Gata3_Day3.3.pTEICM_8

tag: time point


title: GBM13_input

description: GBM  ChIP-seq Input

value: GBM tissue


title: F_P7_normal_CD31_1_DC21_F20

tag: sequencing run

tag: mousename


title: F_P7_normal_CD31_1_DC21_L18

tag: gender

tag: plate

value: Proliferative EC


title: GBM13_H3K27ac

description: GBM  H3K27ac ChIP-seq

tag: chip antibody

value: H3K27ac (Activemotif, #39133)


title: Muscle_Old_biological rep10

value: male


title: Gata3_Day3.3.pTEICM_7

tag: lineage

value: Epiblast


title: F_P21_normal_mesench_1_DC21_K9

tag: well

value: Late Car4- capillaries

tag: coverage


title: GBM12_input

description: GBM  ChIP-seq Input


title: Gata3_Day3.3.pTEICM_6

value: polar


title: Muscle_Old_biological rep8

value: vastus lateralis muscle


title: F_P21_normal_mesench_2_DC21_I22

value: F

tag: timepoint

tag: treatment


title: Muscle_Old_biological rep7


title: F_P7_normal_CD31_1_DC21_I8

tag: cell type

value: Early Car4- capillaries

tag: number of genes


title: GBM11_input

description: GBM  ChIP-seq Input

tag: patient id


title: Gata3_Day3.3.pTEICM_5

value: Blastoid

value: Trophectoderm


title: Muscle_Old_biological rep6

tag: age (y)

tag: disease state

value: healthy


title: Gata3_Day3.3.pTEICM_4

tag: tissue

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_B6

value: distal lung

tag: cell subtype


title: GBM11_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_3

value: Transitioning

tag: time point


title: Gata3_Day3.3.pTEICM_2

value: Primitive Endoderm


title: F_P21_normal_mesench_2_DC21_N12

tag: sequencing run

value: endothelial

tag: mousename

value: normal


title: Muscle_Old_biological rep5

tag: gender


title: F_P21_normal_mesench_1_DC21_F14

tag: plate


title: GBM10_H3K27ac

description: GBM  H3K27ac ChIP-seq

value: GBM tissue

tag: chip antibody

value: H3K27ac (Activemotif, #39133)


title: GBM12_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.3.pTEICM_1

tag: lineage

value: Epiblast


title: F_P7_normal_CD31_1_DC21_O17

tag: well

value: Car4+ capillaries

tag: coverage


title: GBM09_input

description: GBM  ChIP-seq Input


title: Gata3_Day3.2.pTEICM_13

value: polar


title: F_P7_normal_CD31_1_DC21_K10

tag: timepoint

tag: treatment


title: GBM10_input

description: GBM  ChIP-seq Input


title: Muscle_Old_biological rep9

value: male

value: vastus lateralis muscle


title: GBM09_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.2.pTEICM_12


title: Muscle_Old_biological rep3


title: F_P7_normal_CD31_1_DC21_D23

value: F

tag: cell type

tag: number of genes


title: Muscle_Old_biological rep4

tag: age (y)


title: GBM08_input

description: GBM  ChIP-seq Input

tag: patient id


title: Muscle_Old_biological rep2

tag: disease state

tag: tissue


title: F_P7_normal_CD31_1_DC21_K2

tag: cell subtype

value: Venous EC


title: GBM08_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.2.pTEICM_10

value: Blastoid

value: Trophectoderm

tag: time point


title: Muscle_young_biological rep11

source_name: vastus lateralis, young

value: healthy


title: F_P7_normal_CD31_1_DC21_H15

value: distal lung

tag: sequencing run

value: Arterial EC I

tag: mousename


title: Muscle_young_biological rep10

tag: gender


title: Muscle_young_biological rep9


title: F_P7_normal_CD31_1_DC21_H14

tag: plate

value: Proliferative EC


title: GBM07_input

description: GBM  ChIP-seq Input

tag: chip antibody


title: GBM07_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.2.pTEICM_8

tag: lineage

value: 3 days after stem cells seeded to form cell aggregates


title: Gata3_Day3.2.pTEICM_11


title: F_P7_normal_CD31_1_DC21_E21

tag: well

value: endothelial

value: Early Car4- capillaries

tag: coverage

value: normal


title: F_P7_normal_CD31_1_DC21_N16

tag: timepoint

tag: treatment


title: Gata3_Day3.2.pTEICM_9


title: GBM05_input

description: GBM  ChIP-seq Input

value: GBM tissue


title: Muscle_Old_biological rep1


title: Gata3_Day3.2.pTEICM_7


title: Muscle_young_biological rep8


title: F_P7_normal_CD31_1_DC21_H2

tag: cell type

tag: number of genes


title: Gata3_Day3.2.pTEICM_5


title: GBM05_H3K27ac

description: GBM  H3K27ac ChIP-seq

tag: patient id

value: H3K27ac (Activemotif, #39133)


title: F_P7_normal_CD31_1_DC21_F23

value: Late Car4- capillaries


title: Gata3_Day3.2.pTEICM_4

value: polar


title: GBM04_input

description: GBM  ChIP-seq Input


title: Gata3_Day3.2.pTEICM_3


title: Muscle_young_biological rep6

value: male

tag: age (y)

tag: disease state

value: vastus lateralis muscle


title: Muscle_young_biological rep7

tag: tissue


title: F_P7_normal_CD31_1_DC21_A21

value: F

tag: cell subtype


title: Muscle_young_biological rep4


title: Muscle_young_biological rep3


title: Gata3_Day3.2.pTEICM_2

value: Blastoid

tag: time point


title: F_P7_normal_CD31_1_DC21_P23

tag: sequencing run

tag: mousename


title: Muscle_young_biological rep2

tag: gender


title: GBM03_H3K27ac

description: GBM  H3K27ac ChIP-seq

tag: chip antibody


title: Muscle_young_biological rep5


title: F_P7_normal_CD31_1_DC21_F10

tag: plate


title: F_P21_normal_mesench_1_DC21_F17

tag: well


title: Gata3_Day3.1.pTEICM_42

tag: lineage

value: Trophectoderm


title: Gata3_Day3.2.pTEICM_1


title: GBM02_input

description: GBM  ChIP-seq Input


title: GBM04_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: Gata3_Day3.1.pTEICM_41

value: Epiblast


title: F_P7_normal_CD31_1_DC21_D19

value: distal lung

tag: timepoint

tag: coverage


title: Gata3_Day3.1.pTEICM_40


title: GBM02_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: GBM01_H3K27ac

description: GBM  H3K27ac ChIP-seq


title: F_P7_normal_CD31_1_DC21_A5

tag: cell type

tag: treatment


title: Muscle_young_biological rep1

value: healthy


title: GBM01_input

description: GBM  ChIP-seq Input

tag: patient id


title: GBM03_input

description: GBM  ChIP-seq Input


title: F_P7_normal_CD31_1_DC21_K3

tag: number of genes


title: CKO

first: Ting

last: Wu

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Chinese Acadamy of Sciences

data_processing:
Data filtering: The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads were removed before downstream analyses.
Genome mapping: After reads filtering, we map clean reads to reference genome using HISAT.
Gene expression analysis: We map clean reads to reference transcripts using Bowtie2, then calculate gene expression level for each sample with RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: file format: csv; content: Gene expression

source_name: mammary cells

extract_protocol:
About 20,000 luminal cells were harvested and total RNA were extracted by Trizol following standard protocols. Quality control was performed before library construction.
RNA libraries were prepared for sequencing using standard Illumina-HiSeq2500/4000 protocols. RNA-Seq Quantification Library (Low-Input Library)

treatment_protocol: miR-200c/141-flox/flox (Ctrl) and K8-CreERT2;miR-200c/141-flox/flox (CKO) mice were injected with tamoxifen. After 3 days, mammary glands were harvested and digested into single cells, luminal cells were enriched by FACS.

value: primary mammary luminal cells

tag: strain

tag: age

value: 8-weeks old

value: 4-weeks after tamoxifen administration

tag: genotype


title: Gata3_Day3.1.pTEICM_39

tag: tissue

tag: time point

value: 3 days after stem cells seeded to form cell aggregates


title: F_P7_normal_CD31_1_DC21_N3

tag: sequencing run

value: endothelial

tag: cell subtype

value: Venous EC

tag: mousename

value: normal


title: Gata3_Day3.1.pTEICM_38


title: PRDM1α-transduced NK92 cells, biological rep2

city: İzmir

first: Can

last: Küçük

address: Dokuz Eylül University Health Campus, Mithatpaşa Avenue. No: 58/5

department: İzmir Biomedicine and Genome Center

country: Turkey

institute: Dokuz Eylül University

description: Total RNA was purified from PRDM1α-transduced, GFP-sorted NK92 cells 48h post-transduction.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. The arrays were washed and stained in the Affymetrix Fluidics Station 400 using protocol EukGE-WS2v5-450.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner based on the Affymetrix Scanning Protocol.

data_processing: MAS 5.0 Data Processing Protocol. BRB-Array Tools is used for data normalization and log transformation.

label: Biotin

source_name: NK92 cell line

label_protocol: Biotinylated cRNA samples was prepared from 60 ng total RNA according to the standard Affymetrix protocol based on the Expression Analysis Technical Manual (Affymetrix).

growth_protocol: KHYG1 and NK92 cell lines were cultured in the presence of RPMI 1640 medium supplemented with 10 or 20% FBS, penicillin G (100 units/ml), streptomycin (100 g/ml), and 2mM  L-glutamine at 37 °C in 5% CO2. Exogenous rhIL2 (5-7 ng/ml) was included to support growth of these malignant NK cell lines as they are IL2 dependent.

extract_protocol: Total RNA was extracted with TRIzol™ Reagent and further purified with RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of total RNA samples was evaluated by measuring them with spectrophotometre at 260 and 280 nm and running RNA samples within 1X TAE gel.

treatment_protocol: The functional and full-length isoform of PRDM1 (i.e. PRDM1α) was ectopically expressed in NK92 or KHYG1 cells using the PRDM1α-FL-PMIG construct that was available from previous studies. Empty vector (i.e. PMIG) transduced cells were used as the negative controls. Retroviral transduction was performed as described earlier (Küçük et al. PNAS 2011) with the following modifications: 4 μg of empty vector or PRDM1α-FL was co-transfected with 4 μg of PCL-Ampho, the packaging vector, into the 293T cell line. GFP+ cells were FACS-sorted 48h post-transduction.

value: Lymphoid


title: Gata3_Day3.1.pTEICM_37

value: polar


title: Ctrl


title: F_P7_normal_CD31_1_DC21_K1

tag: gender

tag: plate

value: Early Car4- capillaries


title: PRDM1α-transduced NK92 cells, biological rep1


title: Gata3_Day3.1.pTEICM_36

tag: lineage


title: F_P7_normal_CD31_1_DC21_G6

tag: well

tag: timepoint


title: Gata3_Day3.1.pTEICM_35


title: Gata3_Day3.1.pTEICM_34


title: F_P21_normal_mesench_2_DC21_B6

tag: cell type

value: Late Car4- capillaries

tag: coverage


title: PRDM1α-transduced KHYG1 cells, biological rep1

description: Total RNA was purified from PRDM1α-transduced, GFP-sorted KHYG1 cells 48h post-transduction.

source_name: KHYG1 cell line


title: F_P21_normal_mesench_1_DC21_M4

value: F

tag: treatment


title: Gata3_Day3.1.pTEICM_33

value: Blastoid