title: DES_Low (PND22_Des0,003_m89)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m89

value: CACCGG

value: DES


title: DES_Intermediate (PND22_Des0,006_m94)

status: Public on Mar 08 2023

type: SRA

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m94

library_source: transcriptomic

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Rat reference transcriptome from the UCSC website (release rn6, downloaded in August 2020) using BWA version 0.7.4.4  was used to align the second reads
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,483 genes detected.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Ovary

growth_protocol: Time-mated Sprague-Dawley rats were delivered at gestational day (GD) 3. Animals were kept under standard conditions with 12 h light/dark cycles and fed a standard soy- and alfalfa-free diet based on Altromin 1314  along with tap water in Bisphenol A-free bottles provided ad libitum. Animals were kept in pairs until GD17, thereafter individually.

extract_protocol:
RNA was isolated using Kit from Qiagen and stored at -80 ℃.
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.
3'Bulk RNA Barcoding sequencing

treatment_protocol: Rat dams were exposed to DES or KTZ from GD7. The rats were weighed and gavaged each morning with either vehicle control or test substances until three distinct postnatal stages (postnatal days 6, 14, and 22) using three different doses 3, 6 and 12 µg/kg bw/day for DES and 3, 6 and 12 mg/kg bw/day for KTZ.

tag: tissue

value: Ovary

tag: strain

tag: age

tag: genotype

value: wild type

tag: sample well

tag: barcode

value: CAGCGC

tag: treatment

tag: dose

value: 6 µg/kg bw/day


title: K07992496_P3_F3

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute

data_processing:
Alignment was performed with STAR, reads were counted with HTSeq and QC metrics were generated with RNA-SeQC.
The resulting count matrix was filtered by column for samples with more than 10^3 detected genes (counts > 0) and by row for coding genes (as defined by the MGI database) with a row sum across all samples > 500 counts (with a total number of 500 samples). The resulting normalized and filtered count matrix was then variance stabilized using the vst method from the DESeq2 R package. Surrogate variable analysis (SVA, R package) was performed on the vst count matrix to account for linear batch effects.
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: Mouse INsulinoma 6

extract_protocol:
RNA was extracted from cells using TCL buffer (#1031576, Qiagen) with 1% beta-mercaptoethanol followed by an RNA clean-up with Agencourt RNA cleanup XP (#A63987, Beckman Coulter).
Bulk RNA (1 μl) was added to a 3 step cDNA synthesis reaction with 3’RT (5’- AGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’, IDT), template switching (5’-AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’, Qiagen), and ISPCR (5’-AAGCAGTGGTATCAACGCAGAGT-3’, IDT) oligos from the SMART-seq2 protocol 139. cDNA was purified using AMPure XP Agencourt (#100609, Beckman Coulter) and quantified using Qubit dsDNA High Sensitivity (#102689, Life Technologies). Samples were diluted to 0.2 ng/ul in TE and tagmented (Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina). Indexing was performed using the Nextera XT Index Kit (#FC-131-1001, Illumina). Final libraries were QCed using the Qubit dsDNA High Sensitivity kit and Bioanalyzer High Sensitivity DNA Kit (#5067-4627, Agilent).

treatment_protocol: 40,000 MIN6 cells/well were seeded in 96-well plates 24 h prior to treatment in three replicates. FFA library compound plates were transferred into assay plates which were then incubated for 24 h (n=6).

tag: cell line

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(E)-Tetradecenoic acid


title: Asthma patient 153

city: Seoul

first: Ji Eun

last: Lim

address: 26, Kyungheedae-ro, Dongdaemun-gu

department: Department of Biochemistry and Molecular Biology, School of Medicine

country: South Korea

institute: Kyung Hee University

data_processing:
Adapter sequences were trimmed by Trimmomatic (v0.39). Trimmed reads aligned using HISAT2 (v2.2.0) with referring hg19 genome. Aligned reads are sorted by samtools (v1.9). Raw counts of sequencing reads for the features are counted by HTSeq (v0.12.4).
The gene expressions were quantified in transcripts per million (TPM) using GENCODE v19. A gene was allowed for downstream analyses if its expression in at least 20 % of the samples was greater than 0.1 TPM and the read counts were greater than six.
Assembly: hg19
Supplementary files format and content: tab-delimited text file .txt with raw read counts for every sample
Supplementary files format and content: tab-delimited text file .txt with the Transcripts per Million (TPM) values for every sample

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted from PBMC using TRI Reagent solution (Invitrogen, USA) following manufacturer's instructions.
RNA exome sequencing libraries were prepared according to the manufacturer’s instructions (Swift RNA Library Kit and IDT Exome v2.0 kit).

value: peripheral blood mononuclear cells


title: Asthma patient 151


title: DES_High (PND14_Des0,012_m100)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,012_m100

value: AGCCGC

value: 12 µg/kg bw/day


title: Asthma patient 150


title: Asthma patient 155


title: Asthma patient 149


title: K95656032_P3_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: DES_Intermediate (PND14_Des0,006_m96)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,006_m96

value: ACGCGC


title: Asthma patient 147


title: Asthma patient 148


title: CNT_F1_P3_F1

value: 24h 0.5mM BSA


title: BSA_M_P3_E12

value: #N/A


title: DES_Low (PND14_Des0,003_m92)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,003_m92

value: ACCCGG

value: 3 µg/kg bw/day


title: Asthma patient 145


title: Asthma patient 146


title: Asthma patient 143


title: Asthma patient 144


title: DES_Ctrl (PND14_Ctrl_m87)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m87

value: CTCTCC

value: control

value: corn oil (vehicle control)


title: DES_High (PDN6_Des0,012_m98)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m98

value: Ovary

value: wild type

value: TTGTCC

value: DES


title: K18059238_P3_E11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 6(Z), 9(Z), 12(Z)-Octadecatrienoic Acid


title: Asthma patient 142

value: peripheral blood mononuclear cells


title: Asthma patient 139


title: K04565634_P3_E9

value: 24h 0.5mM Octadecanoic acid


title: Asthma patient 140


title: K72611551_P3_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: DES_Low (PND6_Des0,003_m89)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m89

value: GTCAAG


title: Asthma patient 141


title: Asthma patient 137


title: Asthma patient 138


title: DES_Intermediate (PND6_Des0,006_m93)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m93

value: TCCAAC

value: 6 µg/kg bw/day


title: DES_Ctrl (PND6_Ctrl_m85)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m85

value: GGACAT


title: K39965020_P3_E7


title: Asthma patient 135


title: Asthma patient 134


title: Asthma patient 136


title: K07624241_P3_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: DES_High (PND22_Des0,012_m72)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m72

value: GAAGAC

value: 12 µg/kg bw/day


title: DES_Intermediate (PND22_Des0,006_m93)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m93

value: CGACTT


title: Asthma patient 132


title: DES_Low (PND22_Des0,003_m64)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m64

value: Ovary

value: CATCAG

value: 3 µg/kg bw/day


title: Asthma patient 131


title: TUN_3_P3_E8

value: 24h 50ng/ml Tunicamycin


title: Asthma patient 128


title: Asthma patient 129


title: Asthma patient 127


title: Asthma patient 133


title: THP_3_P3_E5

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.00001mM Thapsigargin


title: DES_High (PND14_Des0,012_m98)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,012_m98

value: wild type

value: TTGGAT

value: DES


title: K48097184_P3_E3

value: 24h 0.5mM 11(E)-Octadecenoic acid


title: DES_Intermediate (PND14_Des0,006_m94)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,006_m94

value: TTTTAG


title: Asthma patient 130

value: peripheral blood mononuclear cells


title: CNT_E1_P3_E1

value: 24h 0.5mM BSA


title: Asthma patient 124


title: Asthma patient 125


title: Asthma patient 123


title: K18478158_P3_E4

value: 24h 0.5mM 6(Z), 9(Z), 12(Z), 15(Z)-Octadecatetraenoic acid


title: CNT_D12_P3_D12


title: DES_Low (PND14_Des0,003_m91)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,003_m91

value: TTTATG


title: DES_Ctrl (PND22_Ctrl_m85)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m85

value: ATCGAG

value: control

value: corn oil (vehicle control)


title: K81456670_P3_E2

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: Asthma patient 126


title: Asthma patient 121


title: DES_Ctrl (PND14_Ctrl_m86)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m86

value: Ovary

value: TTGTTA


title: Asthma patient 120


title: DES_High (PDN6_Des0,012_m72)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m72

value: TTCATA

value: 12 µg/kg bw/day


title: Asthma patient 118


title: Asthma patient 119


title: K39534559_P3_D10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Decanoic acid


title: DES_Intermediate (PND6_Des0,006_m68)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m68

value: wild type

value: TTATCA

value: DES

value: 6 µg/kg bw/day


title: Asthma patient 117

value: peripheral blood mononuclear cells


title: Asthma patient 122


title: K84290455_P3_D9

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: DES_Low (PND6_Des0,003_m64)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m64

value: TTACTA

value: 3 µg/kg bw/day


title: DES_Ctrl (PND6_Ctrl_m60)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m60

value: TTAACT

value: control


title: Asthma patient 115


title: Asthma patient 116


title: Asthma patient 114


title: Asthma patient 113


title: Asthma patient 112


title: Asthma patient 110


title: K83944490_P3_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: Asthma patient 111


title: DES_Intermediate (PND22_Des0,006_m68)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m68

value: Ovary

value: TGAATA


title: CNT_D5_P3_D5

value: 24h 0.5mM BSA


title: Asthma patient 108


title: K77749911_P3_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: DES_High (PND22_Des0,012_m71)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m71

value: TGTATT

value: 12 µg/kg bw/day


title: DES_Low (PND22_Des0,003_m63)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m63

value: wild type

value: TCTAAT


title: K00392230_P3_D11

value: Mouse INsulinoma 6 (MIN6)


title: Asthma patient 106


title: Asthma patient 107


title: Asthma patient 104


title: DES_Ctrl (PND22_Ctrl_m60)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m60

value: TCAAAA

value: corn oil (vehicle control)


title: Asthma patient 105

value: peripheral blood mononuclear cells


title: DES_High (PND14_Des0,012_m71)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,012_m71

value: TATTAC

value: DES


title: CNT_D8_P3_D8


title: Asthma patient 103


title: K29160692_P3_D2

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: Asthma patient 109


title: K57491984_P3_D7

value: 24h 0.5mM 6(Z)-Octadecenoic acid


title: DES_Intermediate (PND14_Des0,006_m93)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,006_m93

value: TATCAT

value: 6 µg/kg bw/day


title: CNT_D1_P3_D1


title: Asthma patient 101


title: OA_M_P3_C12

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: Asthma patient 99


title: DES_Low (PND14_Des0,003_m89)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,003_m89

value: Ovary

value: TATAAG

value: 3 µg/kg bw/day


title: Asthma patient 98


title: K80025777_P3_C11

value: 24h 0.5mM 9(Z), 11(E)-octadecadienoic acid


title: DES_Ctrl (PND14_Ctrl_m60)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m60

value: wild type

value: TAGAAT

value: control


title: Asthma patient 97


title: Asthma patient 96


title: Asthma patient 95


title: K98002709_P3_C10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(E)-Nonadecenoic acid


title: DES_High (PDN6_Des0,012_m71)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m71

value: TACAAA

value: 12 µg/kg bw/day


title: DES_Intermediate (PND6_Des0,006_m67)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m67

value: TAATAG

value: DES


title: spinetoram treatment-3 [y3]

city: jinan

first: Yuanxue

last: Yang

state: Shandong

address: No.202 Gongyebei Road

country: China

institute: Shandong Academy of Agricultural Sciences

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: ZJU_Sfru_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Spodoptera frugiperda

source_name: whole body

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: whole body

value: WT

value: treat with spinetoram


title: spinetoram treatment-1 [y1]


title: K20152659_P3_C9

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: Asthma patient 94

value: peripheral blood mononuclear cells


title: cyantraniliprole treatment-3 [x3]

value: treat with cyantraniliprole


title: DES_Low (PND6_Des0,003_m63)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m63

value: Ovary

value: TAACAA

value: 3 µg/kg bw/day


title: spinetoram treatment-2 [y2]


title: Asthma patient 102


title: TUN_2_P3_C8

value: 24h 500ng/ml Tunicamycin


title: K57347788_P3_C7

value: 24h 0.5mM Heneicosanoic acid


title: Asthma patient 92


title: Asthma patient 100


title: cyantraniliprole treatment-2 [x2]


title: DES_Ctrl (PND6_Ctrl_m59)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m59

value: wild type

value: TAAAAC

value: control

value: corn oil (vehicle control)


title: Asthma patient 91


title: K17709609_P3_D3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: Asthma patient 93


title: DES_High (PND22_Des0,012_m70)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m70

value: GTTAAA

value: DES

value: 12 µg/kg bw/day


title: DES_Intermediate (PND22_Des0,006_m67)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m67

value: GATTAA

value: 6 µg/kg bw/day


title: K57739283_P3_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: Asthma patient 90

value: peripheral blood mononuclear cells


title: cyantraniliprole treatment-1 [x1]

value: whole body

value: WT

value: treat with cyantraniliprole


title: tetrazolidamide treatment-3 [s3]

value: treat with tetrazolidamide


title: Asthma patient 89


title: THP_2_P3_C5

value: 24h 0.0001mM Thapsigargin


title: K01624546_P3_C4

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: DES_Ctrl (PND22_Ctrl_m59)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m59

value: Ovary

value: wild type

value: CTTAAT

value: control


title: tetrazolidamide treatment-2 [s2]


title: K47192521_P3_C3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: DES_High (PND14_Des0,012_m70)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,012_m70

value: CTAAAA

value: DES

value: 12 µg/kg bw/day


title: K51131535_P3_C2

value: 24h 0.5mM 9(Z), 12(Z)-Octadecadienoic acid


title: emamectin benzoate treatment-3 [j3]

value: treat with emamectin benzoate


title: DES_Intermediate (PND14_Des0,006_m67)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,006_m67

value: CATAAA

value: 6 µg/kg bw/day


title: K57135146_P3_B11

value: 24h 0.5mM 15(Z)-Tetracosenoic acid


title: emamectin benzoate treatment-2 [j2]

value: whole body

value: WT


title: emamectin benzoate treatment-1 [j1]


title: K33223064_P3_B9

value: 24h 0.5mM Pentadecanoic acid


title: DES_Ctrl (PND14_Ctrl_m59)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m59

value: Ovary

value: ATTGTT

value: corn oil (vehicle control)


title: DES_Low (PND14_Des0,003_m64)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,003_m64

value: wild type

value: ATTTTG

value: 3 µg/kg bw/day


title: control-3 [ck3]

value: control


title: DES_Low (PND22_Des0,003_m62)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m62

value: GAATAT

value: DES


title: control-2 [ck2]


title: CNT_B8_P3_B8

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: Asthma patient 86

value: peripheral blood mononuclear cells


title: Asthma patient 85


title: Asthma patient 84


title: Asthma patient 87


title: Asthma patient 83


title: DES_High (PDN6_Des0,012_m70)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m70

value: ATTATC

value: 12 µg/kg bw/day


title: DES_Intermediate (PND6_Des0,006_m66)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m66

value: ATGTAA

value: 6 µg/kg bw/day


title: K14557781_P3_B7

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: Asthma patient 82


title: control-1 [ck1]

value: whole body

value: WT


title: Asthma patient 81


title: DES_Low (PND6_Des0,003_m62)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m62

value: Ovary

value: ATCTAT


title: tetrazolidamide treatment-1 [s1]

value: treat with tetrazolidamide


title: Asthma patient 88


title: aKG_PD1mAb_4

city: Changsha

first: Nian

last: Liu

state: Hunan

address: Xiangya road 87#

department: Department of Dermatology

institute: Xiangya Hospital, Central South University

data_processing:
Sequencing data filtering：This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution);2) Remove reads whose N content is greater than 5%;3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).The filtered "Clean Reads" are saved in FASTQ format.
After getting clean reads, we used HISAT to align the clean reads to the reference genome.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated from cells or tissues with TRIpure Reagent (Bio Teke, China)
1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform

value: Tumor tissue

tag: cell type

value: melanoma

value: alpha_KG combined with PD1 mAb


title: K96144918_P3_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: K06914719_P3_B10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(E)-Heptadecenoic acid


title: CNT_B5_P3_B5

value: 24h 0.5mM BSA


title: aKG_PD1mAb_3


title: Asthma patient 80

value: peripheral blood mononuclear cells


title: K32862852_P3_B4

value: 24h 0.5mM 12-Methoxydodecanoic acid


title: Asthma patient 79


title: K63913457_P3_B3

value: 24h 0.5mM 11(Z), 14(Z), 17(Z)-Eicosatrienoic Acid


title: aKG_PD1mAb_2


title: Asthma patient 78


title: DES_High (PND22_Des0,012_m69)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,012_m69

value: wild type

value: ATAGAT

value: DES

value: 12 µg/kg bw/day


title: Asthma patient 77


title: K35238727_P3_B2

value: 24h 0.5mM 12(Z) Heneicosenoic acid


title: Asthma patient 76


title: DES_Low (PND22_Des0,003_m61)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,003_m61

value: Ovary

value: AGTATA

value: 3 µg/kg bw/day


title: DES_Ctrl (PND22_Ctrl_m57)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Ctrl_m57

value: AGAATT

value: control

value: corn oil (vehicle control)


title: aKG_PD1mAb_1

value: Tumor tissue

value: melanoma

value: alpha_KG combined with PD1 mAb


title: alpha_KG_3


title: DES_High (PND14_Des0,012_m69)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,012_m69

value: ACTAAA


title: DES_Intermediate (PND22_Des0,006_m65)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND22_Des0,006_m65

value: ATAAGT

value: 6 µg/kg bw/day


title: Asthma patient 74

value: peripheral blood mononuclear cells


title: alpha_KG_2


title: alpha_KG_4


title: K56767655_P3_A10

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Eicosanoic acid


title: alpha_KG_1


title: K25847431_P3_A9

value: 24h 0.5mM 9(E), 12(E)-Octadecadienoic acid


title: Asthma patient 73


title: PD1mAb_4

value: PD1 mAb


title: DES_Ctrl (PND14_Ctrl_m57)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Ctrl_m57

value: Ovary

value: wild type

value: AATATG


title: Asthma patient 72


title: DES_Ctrl (PND6_Ctrl_m58)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m58

value: ATATGA


title: DES_High (PDN6_Des0,012_m65)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PDN6_Des0,012_m65

value: AAGTTA

value: DES

value: 12 µg/kg bw/day


title: PD1mAb_3

value: Tumor tissue

value: melanoma


title: PD1mAb_2


title: Asthma patient 75


title: Asthma patient 71


title: K66986518_P3_A7

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: DES_Intermediate (PND6_Des0,006_m65)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,006_m65

value: AACATA


title: PA_M_P3_A12

value: 24h 0.5mM Hexadecanoic acid


title: DES_Low (PND6_Des0,003_m61)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Des0,003_m61

value: AAATCA

value: 3 µg/kg bw/day


title: THP_1_P3_A5

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.001mM Thapsigargin


title: K18766551_P3_A11

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: DES_Intermediate (PND14_Des0,006_m65)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,006_m65

value: Ovary

value: AATTTC

value: 6 µg/kg bw/day


title: K04327383_P3_A6


title: Vehicle_4

value: Vehicle


title: Asthma patient 69

value: peripheral blood mononuclear cells


title: Asthma patient 70


title: K16120488_P3_A4

value: 24h 0.5mM Tridecanoic acid


title: DES_Low (PND14_Des0,003_m61)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND14_Des0,003_m61

value: wild type

value: AATGTA

value: DES


title: Vehicle_3

value: Tumor tissue

value: melanoma


title: Asthma patient 67


title: Asthma patient 68


title: DES_Ctrl (PND6_Ctrl_m57)

description:
FREIA_WP2_DES.unq.refseq.umi.dat
PND6_Ctrl_m57

value: AAACAT

value: control

value: corn oil (vehicle control)


title: K99906572_P3_A3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(E)-Pentadecenoic acid


title: TUN_1_P3_A8

value: 24h 5000ng/ml Tunicamycin


title: Vehicle_2


title: Asthma patient 66


title: Vehicle_1


title: MCNT_P3_A1

value: 24h Media


title: siRPL18-2-ATAC-48h

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: ATAC-seq

library_source: genomic

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
peaks were called using MACS2 and bigiwg files were produced by deeptools
Assembly: mm9
Supplementary files format and content: narrowPeaks indicating the highly accessible region of the libraries on the Genome
Supplementary files format and content: bigwig file, indicating the enrichment of the libraries on the Genome

molecule: genomic DNA

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.

treatment_protocol: DharmaFECT (Horizon) was used for transfection of siRNA according to the manufacturer’s instructions. cells were harvested for experiments after 3 days of knockdown.

tag: sirna


title: K08446574_P3_A2

value: 24h 0.5mM Nonadecanoic acid


title: CNT_H12_P2_H12

value: 24h 0.5mM BSA


title: Asthma patient 64


title: siRPL14-2-ATAC-48h

description: ATAC-seq


title: Asthma patient 63


title: CNT_H11_P2_H11


title: Asthma patient 65


title: siRPL18-1-ATAC-48h

description: ATAC-seq


title: PD1mAb_1

value: PD1 mAb


title: siRPL14-1-ATAC-48h

description: ATAC-seq


title: K17040651_P2_H10

value: 24h 0.5mM 7(Z), 10(Z), 13(Z), 16(Z)-Docosatetraenoic Acid


title: K03070961_P2_H9

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: Asthma patient 61

value: peripheral blood mononuclear cells


title: siRPL23-2-ATAC-48h

description: ATAC-seq


title: Asthma patient 62


title: siNT-2-ATAC-48h

description: ATAC-seq

value: siNT


title: Pediocin producing CR099 pXMJ19 ped B

type: RNA

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

description: main production phase

hyb_protocol: Agilent hybridisation kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: GeneSpring 14.9 GC, Feature extraction,Baseline Transformation: median of all samples Statistical analysis (moderated t-test, Benjamini-Hochberg FDR, p_corr < 0.1, fold change), export

organism: Corynebacterium glutamicum

source_name: cell biomass

label_protocol: Agilent labeling kit (one color)

growth_protocol: unbaffled 500 mL shake flasks, 50 mL unbuffered complex TY medium containing 20 gL-1 glucose

extract_protocol: mRNA extracted from harvested cell pellets (6 mg DCW) using Qiagen RNeasy kit and Turbo DNAfree kit

treatment_protocol: cells (500 µL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

tag: time

value: Sampling during man pediocin-production phase

value: modified Corynebacterium glutamicum CR099 (pXMJ19 ped)


title: Pediocin producing CR099 pXMJ19 ped A

description: main production phase


title: siNT-1-ATAC-48h

description: ATAC-seq


title: Asthma patient 59


title: Asthma patient 60


title: K67375056_P2_H7

value: 24h 0.5mM Dodecanoic acid


title: siRpl18_48h

data_processing:
Libraries were mapped tomm9 genome using STAR. Only uniquely mapped reads were kept for further analysis.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the FPKM for every gene in every single cell library

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen). Contaminating DNA was removed by DNaseI (Ambion) treatment, and the RNA was further purified using the QIAGEN RNeasy Kit.
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.


title: CNT_H8_P2_H8


title: Pediocin producing CR099 pXMJ19 ped C

description: main production phase


title: K53322389_P2_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: Asthma patient 58


title: Non-pediocin producing CR099 pXMJ19 B

description: main production phase

value: Sampling of non-producing strain in analogous growth phase

value: modified Corynebacterium glutamicum CR099 (pXMJ19)


title: Non-pediocin producing CR099 pXMJ19 C

description: main production phase


title: Non-pediocin producing CR099 pXMJ19 A

description: main production phase


title: siRpl14_48h


title: Asthma patient 57


title: CNT_H5_P2_H5

value: Mouse INsulinoma 6 (MIN6)


title: K32311524_P2_H3

value: 24h 0.5mM 5(Z), 8(Z)-Eicosadienoic acid


title: siRPL23-1-ATAC-48h

description: ATAC-seq


title: Asthma patient 56


title: siRpl11_48h


title: Asthma patient 55


title: siNT_48h


title: siRpl23_48h


title: siRPL14_plus_siDUX-2

data_processing:
Libraries were mapped to mm9 genome using STAR. Only uniquely mapped reads were kept for further analysis.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Assembly: mm9
Supplementary files format and content: Tab delimieted text table containing the FPKM for every gene in every single cell library


title: K80340869_P2_H2

value: 24h 0.5mM Tetradecanoic acid


title: CNT_H1_P2_H1


title: Asthma patient 53


title: p53_WT_MSC_1

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

country: Japan

institute: National Center for Global Health and Medicine

data_processing:
Sequencing was performed using HiSeq1500 (Illumina) with a single-read sequencing length of 60bp. TopHat (version 2.0.13; with default parameters) was used to map the reads to the reference genome (UCSC/mm10) with annotation data from iGenomes (Illumina). Gene expression levels were quantified using Cuffdiff (Cufflinks version 2.2.1; with default parameters), then count data were normalized and batch correction was performed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized count data as well as batch-corrected normalized count data

extract_protocol:
MSCs (CD45-Ter119-CD31-CD140a+LepR+) were sorted into SF-O3 medium, centrifuged at 340 × g for 5 min at 4°C and lysed with 75 μL of RLT buffer + 0.75 μL of β-mercaptoethanol (2-ME). Extraction of total RNA from tumors was performed using TRIzol (15596-018; Invitrogen) according to the manufacturer’s protocol. Extracted RNA was then purified using an RNeasy Mini Kit (QIAGEN)
cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, Palo Alto, CA, USA). ds-cDNA was fragmented using a S220 focused ultrasonicator (Covaris) and cDNA libraries were then generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA).

value: CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cell

value: p53 wildtype

value: Freshly isolated


title: siRPL14_plus_siDUX-1


title: siRPL11_plus_siRPL14-1


title: siNT_plus_siRPL14-2


title: p53_WT_MSC_2


title: PAOA_M_P2_G12

value: 24h 0.5mM Hexadecanoic acid and 9(Z)-Octadecenoic acid


title: siNT_plus_siRPL14-1


title: K46987408_P2_G11

value: 24h 0.5mM Heptadecanoic acid


title: p53_KO_Tumor_6

value: Tumor cell

value: p53 knockout


title: siNT_plus_siRPL11-1


title: Asthma patient 51

value: peripheral blood mononuclear cells


title: K19189338_P2_G9

value: 24h 0.5mM 10-Undecenoic acid


title: Asthma patient 52


title: Asthma patient 49


title: K06763617_P2_H4

value: 24h 0.5mM Undecanoic acid


title: p53_WT_MSC_3


title: Asthma patient 48


title: Asthma patient 54


title: TUN_4_P2_G8

value: 24h 5ng/ml Tunicamycin


title: Asthma patient 47


title: p53_KO_MSC_1


title: siNT_plus_siNT-1


title: siNT_plus_siNT-2


title: K63813237_P2_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: Asthma patient 50


title: Asthma patient 46


title: K38686876_P2_G6

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: Asthma patient 45


title: siNT_plus_siDUX-1


title: THP_4_P2_G5

value: 24h 0.000001mM Thapsigargin


title: p53_KO_MSC_3


title: p53_KO_Tumor_1


title: Asthma patient 44


title: p53_KO_MSC_2


title: K15536865_P2_G4

value: Mouse INsulinoma 6 (MIN6)


title: p53_KO_Tumor_2


title: K43021856_P2_G7

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: C_d100.2

city: Rome

first: Francesca

last: Di Rosa

address: viale Regina Elena 291

country: Italy

institute: Italian National Research Council (CNR)

description:
DIR124A14_R1
100bp single-end reads

data_processing:
Pre-processed with nfcore/rnaseq v3.0 using STAR/RSEM.
Analyse log fold changes with DESeq2 v1.30.1.
Assembly: GRCm38/release-95
Supplementary files format and content: .genes.results.txt files are RSEM-STAR-quantified raw counts, TPM values, and FPKM values.
Supplementary files format and content: differential' files are Excel spreadsheets of all inferential properties.

source_name: spleen

growth_protocol: Female BALB/c mice were primed i.m. in the quadriceps with ChAd3‐gag (107 vp) at day (d) 0.

extract_protocol:
Cells were centrifuged and pellets resuspended in Buffer RLT Plus (RNeasy Plus Mini Kit from Qiagen, Germantown, MD, USA), and frozen at -80°C. Total RNA was isolated using QIAcube HT according to manufacturer instructions.
cDNA libraries were prepared using NEBNext Single Cell/Low Input Library Prep Kit (from 2ng RNA normalised input), following manufacturer’s instructions.
The NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina uses a template switching method to generate full length cDNAs directly from single cells or 2 pg – 200 ng RNA, followed by conversion to sequence-ready libraries using the Ultra™ II FS workflow.

treatment_protocol: At either d30 or d100 post-prime, CD8 T cells were enriched from pooled Red Blood Cells-lysed spleen cells of 12 primed mice by negative selection with Dyna Beads magnetic beads (Thermo Fisher Scientific). Enriched CD8 T cells were stained with Tetr-gag APC, Pent-gag PE, anti-CD3 PerCP-Cy5.5, anti-CD8α FITC mAbs, and viability dye eFluor780. Then live Tetr-gag+Pent-gag+CD3+CD8+ cells were sorted by flow cytometry into PBS buffer 1% BSA 2mM EDTA using BD Aria instrument, and retained on ice. FACS-sorted cells were confirmed to be 93% pure on average prior to RNA extraction.

value: Balb/c

tag: Sex

value: female

value: spleen

value: gag-specific CD8 T cells

tag: mouse treatment

value: prime with ChAd3-gag

tag: time (ndays)

tag: experiment

value: C

tag: experimental group


title: C_d100.1

description:
DIR124A12_R1
100bp single-end reads

tag: tissue


title: K75918321_P2_G3

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: Hel3_4

type: genomic

city: Newcaslte upon Tyne

first: James

middle: Mark

last: Allan

address: Herschel Building

country: United Kingdom

institute: Newcastle University

description: HEL AML cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: HEL AML cell clone

label_protocol: Standard Illumina Protocol

growth_protocol: HEL AML cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol: genomic DNA was extracted and purified from HEL AML cell line samples using Qiagen DNeasy Kit according to standard instructions

tag: tet2 mutation

value: TET2 biallelic mutation


title: HelC5

description: HEL AML cell line

value: TET2 monoallelic mutation


title: HelC3

description: HEL AML cell line


title: Asthma patient 43

value: peripheral blood mononuclear cells


title: Asthma patient 42


title: p53_KO_Tumor_4

value: Tumor cell

value: p53 knockout

value: Freshly isolated


title: K80325895_P2_G2

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: Hel7_16

description: HEL AML cell line


title: Hel7_58

description: HEL AML cell line


title: D_d30

description:
DIR124A1_R1
100bp single-end reads

tag: strain

value: D


title: B_d100

description:
DIR124A8_R1
100bp single-end reads

value: B


title: K91356052_P2_F11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: Asthma patient 41


title: Asthma patient 39


title: C_d30

description:
DIR124A10_R1
100bp single-end reads

value: Balb/c

value: female


title: CNT_G1_P2_G1

value: 24h 0.5mM BSA


title: Asthma patient 40


title: CNT_F12_P2_F12


title: glycyrrhizic acid+gefitinib,16 days,3

city: Zhengzhou

first: Shuaifei

last: Lu

state: Henan

address: Jinshui East Road 156

institute: Henan University of Chinese Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Mouse livers were stored in a -80 degree Celsius refrigerator and transported and stored in liquid nitrogen.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: sanitary saline, gefitinib， glycyrrhizic acid+gefitinib，16days

value: liver

value: glycyrrhizic acid+gefitinib

value: 16 days


title: Asthma patient 38


title: Hel3_3

description: HEL AML cell line

value: TET2 biallelic mutation


title: glycyrrhizic acid+gefitinib,16 days,2


title: B_d30

description:
DIR124A6_R1
100bp single-end reads

value: spleen

value: gag-specific CD8 T cells

value: prime with ChAd3-gag


title: A_d30

description:
DIR124A2_R1
100bp single-end reads

value: A


title: glycyrrhizic acid+gefitinib,16 days,1


title: K57416915_P2_F10

value: 24h 0.5mM 6(E)-Octadecenoic acid


title: gefitinib,16 days,2

source_name: liver,gefitinib,16 days,2

value: gefitinib


title: siRpl14_plus_siRpl11_2

data_processing:
Libraries were mapped tomm9 genome using STAR. Only uniquely mapped reads were kept for further analysis.
Genes were quantified using Cuffquant.
Libraries were normalized using Cuffnorm.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimieted text table containing the FPKM for every gene in every single cell library


title: Asthma patient 37

value: peripheral blood mononuclear cells


title: p53_KO_Tumor_5

value: Tumor cell

tag: genotype

value: p53 knockout

value: Freshly isolated


title: siRpl14_plus_siRpl11_1


title: Asthma patient 36


title: CNT_F8_P2_F8

value: Mouse INsulinoma 6 (MIN6)


title: gefitinib,16 days,1

source_name: liver,gefitinib,16 days,1


title: siRpl14_plus_siDux


title: Asthma patient 35


title: K33396764_P2_F7

value: 24h 0.5mM 9(Z), 12(Z), 15(Z)-Octadecatrienoic Acid


title: Sanitary saline,16 days,3

source_name: liver,Sanitary saline,16 days,3

value: Sanitary saline


title: siNT_plus_siRpl14


title: CNT_F5_P2_F5

value: 24h 0.5mM BSA


title: Sanitary saline,16 days,2

source_name: liver,Sanitary saline,16 days,2

value: liver


title: K71795348_P2_F6

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: Sanitary saline,16 days,1

source_name: liver,Sanitary saline,16 days,1

value: 16 days


title: gefitinib,16 days,3

source_name: liver,gefitinib,16 days,3


title: K43930766_P2_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: Asthma patient 33


title: siNT_plus_siRpl14_2


title: control_S5722Nr7

city: New York

first: Anna

last: Gaponova

address: 345 Park Avenue South

institute: Insilico Medicine

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014). Quality trimming of the reads has not been performed.
RNA-Seq: Trimmed raw reads were aligned to rn5 using STAR (version 2.7.3) (Dobin et al. 2013).
Differential expression analysis between groups was performed with DESeq2 (version 1.24.0) (Love et al. 2014) in R (version 3.6.1) (R Core Team 2015). DESeq2 uses a negative binomial generalized linear model to test for differential expression based on gene counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney cortex

extract_protocol:
RNA extracted from microdissected proximal tubules of Ctns knockout mouse kidneys and controls. RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
Library Preparation Kit: TruSeq Stranded mRNA (Illumina)

value: kidney cortex

value: proximal tubule cells

value: CTNS WT


title: siNT_plus_siRpl14_1


title: K07992496_P2_F3

value: 24h 0.5mM 9(E)-Tetradecenoic acid


title: control_S5722Nr4


title: Asthma patient 32


title: Asthma patient 31


title: Asthma patient 34


title: K65207153_P2_F4

value: 24h 0.5mM 5(Z),8(Z)-7Dimethyleicosadienoic acid


title: Asthma patient 30

value: peripheral blood mononuclear cells


title: siNT_plus_siRpl11_1


title: control_S5722Nr2


title: siNT_plus_siRpl11_2


title: CNT_F1_P2_F1


title: Asthma patient 29


title: siNT_plus_siNT


title: K95656032_P2_F2

value: 24h 0.5mM 7(E)-Nonadecenoic acid


title: control_S5722Nr1


title: siNT_plus_siNT_2


title: Asthma patient 28


title: BSA_M_P2_E12

value: #N/A


title: siNT_plus_siNT_1


title: K72611551_P2_E10

value: 24h 0.5mM 13(Z)-Docosenoic acid


title: case_S5722Nr8

value: CTNS KO


title: siNT_plus_siDux


title: Asthma patient 26


title: case_S5722Nr6


title: ileum 8:00 am rep2

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

description: immunoprecipitated genomic DNA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
samples were pre-processed with Cutadapt (Martin et al., 2011) v1.13 to remove the first 9 nucleotides and to trim trailing polyT sequences for at least 10 T’s
The reads were aligned to the mm9 revision of the mouse reference genome using only annotated chromosomes 1-19, chrX, chrY and chrM. Alignment was performed using Bowie (Langmead et al., 2009) with parameters -m 1 –strata –best-y-S - 40.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized Bigwig files were generated using homer make UCSC file v4.9.1 (Heinz et al., 2010) with the following parameters ‘-norm 1e7’

source_name: Immunoprecipitated DNA using 5-methyl cytosine antibody from ileum

extract_protocol:
MeDIP assay was performed using freshly isolated ileum from wild type mice at 8:00am (ZT02) and 8:00 pm( ZT14). Genomic DNA was prepared using phenol chloroform extraction method, purified and sonicated. The sonicated DNA was used for immunoprecipitation using 5 methyl cytosine antibody. The immunoprecipitated DNA was used for MeDIP-seq and analysis.
Librairies were prepared using the SMART cDNA Library Construction Kit and sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.

value: distal ileum

value: wild type

tag: time point


title: case_S5722Nr5


title: TUN_3_P2_E8

value: Mouse INsulinoma 6 (MIN6)

value: 24h 50ng/ml Tunicamycin


title: ileum 8:00 am rep1

description: immunoprecipitated genomic DNA


title: K39965020_P2_E7


title: case_S5722Nr3


title: Asthma patient 25


title: Asthma patient 24


title: K07624241_P2_E6

value: 24h 0.5mM 13(E)-Docosenoic acid


title: Asthma patient 23


title: ileum 8:00 pm rep2

description: immunoprecipitated genomic DNA


title: Asthma patient 22


title: ileum 8:00 pm rep1

description: immunoprecipitated genomic DNA


title: THP_3_P2_E5

value: 24h 0.00001mM Thapsigargin


title: Asthma patient 27


title: K18478158_P2_E4

value: 24h 0.5mM 6(Z), 9(Z), 12(Z), 15(Z)-Octadecatetraenoic acid


title: siRpl23-48h-2

tag: age


title: Asthma patient 21


title: K48097184_P2_E3

tag: treatment

value: 24h 0.5mM 11(E)-Octadecenoic acid


title: K04565634_P2_E9

value: 24h 0.5mM Octadecanoic acid


title: Asthma patient 20


title: Tumor tissue from the IP+LC model-02

city: Hiroshima

first: Kiyofumi

last: Shimoji

address: 1-2-3, Kasumi, Minami-ku

department: Molecular and Internal Medicine, Graduate School of Biomedical and Health Sciences

institute: Hiroshima University

data_processing:
Read1 (barcode read) was extracted by using UMI-tools (ver.1.1.1) with the following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC --read2-stdout ”.
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver. 0.6.7).
Reads were mapped to the GRCm38 reference using HISAT2 (ver. 2.2.1).
Read counts for each gene was obtained by featureCounts (ver. 2.0.1) and UMI duplication is removed by UMI-tools with following command “umi_tools count --method=unique --per-gene --per-cell --gene-tag=XT”.
Assembly: GRCm38
Supplementary files format and content: DESeq2 normalized count

source_name: Tumor tissue from Lung

extract_protocol:
The tumor tissues of the LC model and the IP + LC model were homogenized using 1 mL TRIzol reagent (Life Technologies) and total RNA was extracted using the RNeasy Mini Kit (Qiagen). 180ng of total RNA was used for the construction of sequencing libraries.
Barcoded oligo-dT based primer (5’-GCCGGTAATACGACTCACTATAGGGAGTTCTACAGTCCGACGATCNNNNNNNNNNCCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTV -3’ ; (10)N=UMI, (9)C=cell barcode) was used for single-stranded cDNA synthesis and Second Strand Synthesis Module (NEB, #E6111) was used for double-stranded cDNA synthesis. In-house MEDS-B Tn5 transposase was used for tagmentation and libraries were amplified by 10 cycles of PCR using Phusion High-Fidelity DNA Polymerase (Thermo Scientific, #M0530) and following primers (5’-AATGATACGGCGACCACCGAGATCTACACindexGTTCAGAGTTCTACAGTCCGA-3',5’-CAAGCAGAAGACGGCATACGAGATindex GTCTCGTGGGCTCGGAGATGT-3').

value: Tumor tissue from Lung

value: Lewis lung carcinoma

value: Lung cancer cells

value: WT


title: siRpl18-48h-2


title: Tumor tissue from the IP+LC model-01


title: Tumor tissue from the IP+LC model-03


title: Tumor tissue from the LC model-02


title: siRpl18-48h-1


title: Asthma patient 19

value: peripheral blood mononuclear cells


title: CNT_E1_P2_E1

value: 24h 0.5mM BSA


title: B1-8 BTKWT V9

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
barcodes.tsv
features.tsv
umiDedup-Exact.mtx

library_source: transcriptomic single cell

data_processing:
The gene count matrix was generated by aligning raw reads to the mouse genome (GRCm39 release 107) using STARsolo 2.7.10a and requiring a simple overlap with a gene region (Genefull).
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv, features.tsv, umiDedup-Exact.mtx

source_name: lymph node

extract_protocol:
Single LZ B cells were sorted into 5 uL of TCL Buffer (Qiagen). RNA was purified using magnetic beads (RNAclean XP, Beckman Coulter)
Template-switched cDNA was generated and pre-amplified. Tagmentation was performed with an Illumina DNA Prep kit and indexed using IDT for Illumina Index Sets.
SMART-Seq2

treatment_protocol: Mice were treated with acalabrutinib or vehicle (see paper for details).

value: lymph node

value: Germinal Center LZ B cells

value: B1-8hi BTKWT

value: Vehicle


title: CNT_D12_P2_D12

data_processing:
Alignment was performed with STAR, reads were counted with HTSeq and QC metrics were generated with RNA-SeQC.
The resulting count matrix was filtered by column for samples with more than 10^3 detected genes (counts > 0) and by row for coding genes (as defined by the MGI database) with a row sum across all samples > 500 counts (with a total number of 500 samples). The resulting normalized and filtered count matrix was then variance stabilized using the vst method from the DESeq2 R package. Surrogate variable analysis (SVA, R package) was performed on the vst count matrix to account for linear batch effects.
Assembly: mm10

source_name: Mouse INsulinoma 6

value: Mouse INsulinoma 6 (MIN6)


title: K81456670_P2_E2

value: 24h 0.5mM 11(Z)-Eicosenoic acid


title: siRpl14-48h-1


title: Asthma patient 16

data_processing:
Adapter sequences were trimmed by Trimmomatic (v0.39). Trimmed reads aligned using HISAT2 (v2.2.0) with referring hg19 genome. Aligned reads are sorted by samtools (v1.9). Raw counts of sequencing reads for the features are counted by HTSeq (v0.12.4).
The gene expressions were quantified in transcripts per million (TPM) using GENCODE v19. A gene was allowed for downstream analyses if its expression in at least 20 % of the samples was greater than 0.1 TPM and the read counts were greater than six.
Assembly: hg19
Supplementary files format and content: tab-delimited text file .txt with raw read counts for every sample
Supplementary files format and content: tab-delimited text file .txt with the Transcripts per Million (TPM) values for every sample

source_name: peripheral blood mononuclear cells


title: Asthma patient 18


title: siRpl14-48h-2


title: Asthma patient 17


title: siRpl23-48h-1


title: K84290455_P2_D9

value: 24h 0.5mM 5(Z)-Eicosenoic acid


title: B1-8 BTKWT V7


title: siRpl11-48h-1


title: Asthma patient 14


title: K39534559_P2_D10

value: 24h 0.5mM Decanoic acid


title: B1-8 BTKWT V5


title: Tumor tissue from the LC model-03


title: siRpl11-48h-2


title: B1-8 BTKWT A7

value: Acalabrutinib


title: K83944490_P2_D6

value: 24h 0.5mM 14(E)-Tricosenoic acid


title: B1-8 BTKWT A8


title: Tumor tissue from the LC model-01


title: Asthma patient 15


title: B1-8 BTKWT A11


title: K57491984_P2_D7

value: 24h 0.5mM 6(Z)-Octadecenoic acid


title: Asthma patient 13


title: Asthma patient 11


title: siNT-48h-1


title: siNT-48h-2


title: P80-F-WT3: P80-female-wildtype replicate3

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole brain

value: female

value: wildtype


title: B1-8 BTKWT A10


title: CNT_D8_P2_D8


title: Asthma patient 10


title: K77749911_P2_D4

value: 24h 0.5mM 11-Dodecenoic acid


title: Asthma patient 9

value: peripheral blood mononuclear cells


title: K17709609_P2_D3

value: 24h 0.5mM 10(Z)-Pentadecenoic acid


title: B1-8 BTKC481S V7

value: lymph node

value: B1-8hi BTKC481S


title: B1-8 BTKWT A12

value: Germinal Center LZ B cells

value: B1-8hi BTKWT


title: B1-8 BTKC481S V9

value: Vehicle


title: Asthma patient 12


title: P80-F-HT3: P80-female-hetero replicate3

value: hetero


title: Asthma patient 8


title: K29160692_P2_D2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(E)-Hexadecenoic acid


title: B1-8 BTKC481S V5


title: P80-F-HT2: P80-female-hetero replicate2


title: CNT_D1_P2_D1

value: 24h 0.5mM BSA


title: Asthma patient 7


title: B1-8 BTKC481S A8

value: Acalabrutinib


title: P80-F-HT1: P80-female-hetero replicate1


title: B1-8 BTKC481S A7


title: Asthma patient 6


title: P80-M-WT3: P80-male-wildtype replicate3

value: male


title: OA_M_P2_C12

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: P80-F-WT2: P80-female-wildtype replicate2

value: whole brain

value: female


title: Asthma patient 5


title: B1-8 BTKC481S A12


title: K98002709_P2_C10

value: 24h 0.5mM 10(E)-Nonadecenoic acid


title: P80-M-WT2: P80-male-wildtype replicate2

value: wildtype


title: P80-F-WT1: P80-female-wildtype replicate1


title: siNT_plus_siDUX-2


title: Asthma patient 4

value: peripheral blood mononuclear cells


title: K20152659_P2_C9

value: 24h 0.5mM 8(Z), 11(Z), 14(Z)-Eicosatrienoic Acid


title: TUN_2_P2_C8

value: 24h 500ng/ml Tunicamycin


title: B1-8 BTKC481S A11

value: lymph node

value: Germinal Center LZ B cells

value: B1-8hi BTKC481S


title: Asthma patient 2


title: K57347788_P2_C7

value: 24h 0.5mM Heneicosanoic acid


title: p53_KO_Tumor_3

value: Tumor cell

value: p53 knockout

value: Freshly isolated


title: P80-M-WT1: P80-male-wildtype replicate1


title: B1-8 BTKC481S A10

value: Acalabrutinib


title: P80-M-HT2: P80-male-hetero replicate2

value: male

value: hetero


title: P80-M-HT3: P80-male-hetero replicate3

value: whole brain


title: Asthma patient 1


title: CNT_D5_P2_D5

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: Asthma patient 3


title: K57739283_P2_C6

value: 24h 0.5mM 12-Tridecenoic acid


title: LZ_mNnP_11

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
F7

data_processing:
Kallisto (v.0.44) was used to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 94). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis.
Assembly: GRCm38
Supplementary files format and content: Excel files with abundance and differential expression

extract_protocol:
GC B cells (400 cells/sample) were sorted into 25 uL TCL Buffer (Qiagen). RNA was purified using magnetic beads (RNACleanXP, Beckman Coulter).
Template-switched cDNA was generated and pre-amplified. Tagmentation was performed using a Nextera XT DNA Library Prep kit (Illumina) and indexed using Nextera XT Index Kit v2 Set A (Illumina).
SMART-Seq2

value: B1-8hi c-Myc-GFP


title: P25-F-WT3: P25-female-wildtype replicate3

value: female

value: wildtype


title: K01624546_P2_C4

extract_protocol:
RNA was extracted from cells using TCL buffer (#1031576, Qiagen) with 1% beta-mercaptoethanol followed by an RNA clean-up with Agencourt RNA cleanup XP (#A63987, Beckman Coulter).
Bulk RNA (1 μl) was added to a 3 step cDNA synthesis reaction with 3’RT (5’- AGCAGTGGTATCAACGCAGAGTAC(T30)VN-3’, IDT), template switching (5’-AAGCAGTGGTATCAACGCAGAGTACrGrG+G-3’, Qiagen), and ISPCR (5’-AAGCAGTGGTATCAACGCAGAGT-3’, IDT) oligos from the SMART-seq2 protocol 139. cDNA was purified using AMPure XP Agencourt (#100609, Beckman Coulter) and quantified using Qubit dsDNA High Sensitivity (#102689, Life Technologies). Samples were diluted to 0.2 ng/ul in TE and tagmented (Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina). Indexing was performed using the Nextera XT Index Kit (#FC-131-1001, Illumina). Final libraries were QCed using the Qubit dsDNA High Sensitivity kit and Bioanalyzer High Sensitivity DNA Kit (#5067-4627, Agilent).

value: 24h 0.5mM 13(Z), 16(Z), 19(Z)-Docosatrienoic acid


title: P25-F-WT2: P25-female-wildtype replicate2


title: THP_2_P2_C5

value: 24h 0.0001mM Thapsigargin


title: LZ_mPnN_05

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
F5

value: lymph node

value: Germinal Center LZ B cells


title: K47192521_P2_C3

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)-Eicosapentaenoic acid


title: P25-F-WT1: P25-female-wildtype replicate1


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA PI, biol rep 3

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

address: 1 Barker Hall #3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
rna_pelo_3
pelokd_p1_mrna_grch38_cnt_all.csv

data_processing:
Ribosome profiling reads were first trimmed using Cutadapt to remove adapter sequences.
Trimmed ribosome footprint reads and RNA-Seq reads were then aligned to ribosomal, transfer and noncoding RNA references. The remaining reads were subsequently aligned to the GRCh38 transcriptome using STAR.
Footprint and RNA-Seq transcript abundance were quantified from these alignments by RSEM.
Assembly: hg18
Supplementary files format and content: Comma-delimited text file containing raw, unnormalized read counts for each sample.

growth_protocol: Human K562 cells were grown in RPMI-1640 with L-glutamine (ThermoFisher Scientific) supplemented with 10% FBS, 1% sodium pyruvate, 100 units/mL penicillin and 100 mg/mL streptomycin and grown at 37C and 5% CO2.

extract_protocol:
30ug of RNA for ribosome profiling was harvested by TRIzol extraction; 1ug of RNA for RNA-seq was harvested by phenol-chloroform extraction.
Ribosome footprint libraries were prepared by PCR amplifcation from circularized cDNA using NEBNext Multiplex oligos; matched RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer's protocol.

value: myeloid leukemia cells

value: PELO knockdown

value: PI


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA PI, biol rep 2

description:
rna_pelo_2
pelokd_p1_mrna_grch38_cnt_all.csv


title: LZ_mNnN_10

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
F4


title: AD

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

institute: Cardiff University

data_processing:
CellRanger (v4.0.0, 10x Genomics) was used to map raw sequencing reads to the reference genome (refdata-gex-GRCh38-2020-A), which was modified according to 10x instructions as a pre-mRNA reference to also count intronic reads. The filtered feature-barcode matrices were used as input to downstram processing by the Seurat R package (v4.3.0).
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 from Cell Ranger count output containing gene-cell barcode matrices in HDF5 format

source_name: brain frontal cortex

extract_protocol:
Frozen human brain tissues were thawed on ice followed by a microvessel-enrichment protocol: meninges were removed, tissue was homogenised , centrifuged and filtered using a 300µm and 40µm strainer. Isolated microvessels were washed, pelleted and subjected to nuclei isolation through a series of homogenisation in nuclei isolation buffer, incubation and centrifugation. Cell lysis to obtain positive nuclei was monitored by Trypan blue and nuclei (DAPI) were isolated by filtration through a 30µm cell strainer. Fluorescence activated cell sorting (FACS) gating strategy obtained single nuclei which were then inserted in the 10x Chromium platform.
The Chromium Single Cell 3' single cell RNAseq version 3 reagent kit (10x Genomics) was used. Nuclei were loaded onto each channel of the Chromium Chip G following manufacturer’s instructions and the chip was inserted in the Chromium Controller for droplet encapsulation.  Following GEM generation and barcoding, cDNA amplification was performed for 12 cycles, and gene expression library construction using 14 cycles of sample index PCR was performed according to manufacturer’s protocol (CG000204). Single nuclei gene expression libraries were then sequenced on the Illumina NovaSeq 6000 system at a targeted depth of at least 50,000 reads per nucleus, using the following parameters: Read1: 28bp i7:8bp, Read2: 98bp cycles.

value: brain frontal cortex

tag: disease

value: Alzheimer's disease

value: M


title: CT

value: healthy control

value: F


title: LZ_mNnN_11

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
F8

tag: cell line


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA PI, biol rep 1

description:
rna_pelo_1
pelokd_p1_mrna_grch38_cnt_all.csv

tag: cell type


title: K06914719_P2_B10

city: Cambridge

first: Matthew

last: Brown

address: 75 Ames St

institute: Broad Institute

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(E)-Heptadecenoic acid


title: LZ_mPnP_04

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
F2

value: B1-8hi c-Myc-GFP


title: P80-M-HT1: P80-male-hetero replicate1

value: whole brain

value: male

value: hetero


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA PI, biol rep 3

description:
rna_neg_3
pelokd_p1_mrna_grch38_cnt_all.csv

value: WT


title: P25-F-HT1: P25-female-hetero replicate1

value: female


title: LZ_mNnP_10

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
F3

value: lymph node

value: Germinal Center LZ B cells


title: CNT_B12_P2_B12

value: 24h 0.5mM BSA


title: LZ_mNnN_09

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
E8


title: LZ_mPnN_04

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
F1


title: P25-F-HT3: P25-female-hetero replicate3


title: P25-M-WT3: P25-male-wildtype replicate3

value: wildtype


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA PI, biol rep 2

description:
rna_neg_2
pelokd_p1_mrna_grch38_cnt_all.csv

value: myeloid leukemia cells

value: PI


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA PI, biol rep 1

description:
rna_neg_1
pelokd_p1_mrna_grch38_cnt_all.csv


title: P25-M-WT2: P25-male-wildtype replicate2


title: K14557781_P2_B7

value: 24h 0.5mM 9(Z)-Octadecenoic acid


title: LZ_mPnP_03

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
E6


title: K562 CEBPA reporter cell line, PELO sgRNA ribo PI, biol rep 3

description:
rpf_pelo_3
pelokd_p1_ribo_cds_grch38_cnt_all.csv

data_processing:
Ribosome profiling reads were first trimmed using Cutadapt to remove adapter sequences.
Trimmed ribosome footprint reads and RNA-Seq reads were then aligned to ribosomal, transfer and noncoding RNA references. The remaining reads were subsequently aligned to the GRCh38 transcriptome using STAR.
Footprint and RNA-Seq transcript abundance were quantified from these alignments by RSEM.
Assembly: hg18
Supplementary files format and content: Comma-delimited text file containing raw, unnormalized read counts for each sample.
Library strategy: Ribo-Seq

value: PELO knockdown


title: P25-M-WT1: P25-male-wildtype replicate1


title: CNT_B5_P2_B5


title: P25-M-HT3: P25-male-hetero replicate3


title: K562 CEBPA reporter cell line, PELO sgRNA ribo PI, biol rep 2

description:
rpf_pelo_2
pelokd_p1_ribo_cds_grch38_cnt_all.csv


title: K562 CEBPA reporter cell line, PELO sgRNA ribo PI, biol rep 1

description:
rpf_pelo_1
pelokd_p1_ribo_cds_grch38_cnt_all.csv


title: P25-F-HT2: P25-female-hetero replicate2


title: LZ_mPnN_03

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
E5


title: K33223064_P2_B9

value: 24h 0.5mM Pentadecanoic acid


title: K63913457_P2_B3

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z), 14(Z), 17(Z)-Eicosatrienoic Acid


title: K32862852_P2_B4

value: 24h 0.5mM 12-Methoxydodecanoic acid


title: LZ_mNnN_08

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
E4

value: B1-8hi c-Myc-GFP


title: P25-M-HT2: P25-male-hetero replicate2

value: whole brain

value: male


title: LZ_mNnP_08

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
E3


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo PI, biol rep 2

description:
rpf_neg_2
pelokd_p1_ribo_cds_grch38_cnt_all.csv

value: WT


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo PI, biol rep 3

description:
rpf_neg_3
pelokd_p1_ribo_cds_grch38_cnt_all.csv


title: P0-F-WT3: P0-female-wildtype replicate3

value: female


title: LZ_mNnP_09

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
E7

value: lymph node


title: K35238727_P2_B2

value: 24h 0.5mM 12(Z) Heneicosenoic acid


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo PI, biol rep 1

description:
rpf_neg_1
pelokd_p1_ribo_cds_grch38_cnt_all.csv


title: LZ_mPnP_02

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
E2

value: Germinal Center LZ B cells


title: LZ_mPnN_02

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
E1


title: K96144918_P2_B6

value: 24h 0.5mM 5(Z), 8(Z), 11(Z)-Eicosatrienoic Acid


title: P0-F-WT2: P0-female-wildtype replicate2

value: wildtype


title: P25-M-HT1: P25-male-hetero replicate1

value: hetero


title: PA_M_P2_A12

value: 24h 0.5mM Hexadecanoic acid


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA RNAseI, biol rep 3

description:
rna_pelo_3
pelokd_rnase1_mrna_grch38_cnt_all.csv

value: myeloid leukemia cells

value: PELO knockdown

value: RNAseI


title: K18766551_P2_A11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z)-Octadecenoic acid


title: P0-F-WT1: P0-female-wildtype replicate1


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA RNAseI, biol rep 1

description:
rna_pelo_1
pelokd_rnase1_mrna_grch38_cnt_all.csv


title: P0-F-HT3: P0-female-hetero replicate3


title: LZ_mNnN_07

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
D8

value: B1-8hi c-Myc-GFP


title: K562 CEBPA reporter cell line, PELO sgRNA mRNA RNAseI, biol rep 2

description:
rna_pelo_2
pelokd_rnase1_mrna_grch38_cnt_all.csv


title: K25847431_P2_A9

value: 24h 0.5mM 9(E), 12(E)-Octadecadienoic acid


title: K56767655_P2_A10

value: 24h 0.5mM Eicosanoic acid


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA RNAseI, biol rep 3

description:
rna_neg_3
pelokd_rnase1_mrna_grch38_cnt_all.csv

value: WT


title: TUN_1_P2_A8

value: 24h 5000ng/ml Tunicamycin


title: LZ_mPnP_01

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
D6

value: lymph node


title: K66986518_P2_A7

value: 24h 0.5mM 8(Z)-Eicosenoic acid


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA RNAseI, biol rep 2

description:
rna_neg_2
pelokd_rnase1_mrna_grch38_cnt_all.csv


title: LZ_mPnN_01

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
D5

value: Germinal Center LZ B cells


title: K562 CEBPA reporter cell line, nontargeting sgRNA mRNA RNAseI, biol rep 1

description:
rna_neg_1
pelokd_rnase1_mrna_grch38_cnt_all.csv


title: LZ_mNnP_07

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
D7


title: P0-M-WT2: P0-male-wildtype replicate2

value: whole brain

value: male


title: LZ_mNnN_06

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
D4


title: K04327383_P2_A6


title: P0-M-WT3: P0-male-wildtype replicate3

value: wildtype


title: K562 CEBPA reporter cell line, PELO sgRNA ribo RNAseI, biol rep 3

description:
rpf_pelo_3
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv


title: P0-F-HT1: P0-female-hetero replicate1

value: female

value: hetero


title: P0-F-HT2: P0-female-hetero replicate2


title: DZ_mNnP_06

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
C6

value: Germinal Center DZ B cells


title: P0-M-WT1: P0-male-wildtype replicate1


title: DZ_mNnN_07

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
D1


title: DZ_mNnP_07

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
D2


title: K562 CEBPA reporter cell line, PELO sgRNA ribo RNAseI, biol rep 1

description:
rpf_pelo_1
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv

value: myeloid leukemia cells

value: PELO knockdown

value: RNAseI


title: P0-M-HT3: P0-male-hetero replicate3


title: K16120488_P2_A4

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tridecanoic acid


title: LZ_mNnP_06

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
C7

value: B1-8hi c-Myc-GFP


title: K08446574_P2_A2

value: 24h 0.5mM Nonadecanoic acid


title: K562 CEBPA reporter cell line, PELO sgRNA ribo RNAseI, biol rep 2

description:
rpf_pelo_2
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv


title: DZ_mNnN_06

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
C5


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo RNAseI, biol rep 2

description:
rpf_neg_2
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv

value: WT


title: MCNT_P2_A1

value: 24h Media


title: P0-M-HT1: P0-male-hetero replicate1


title: CNT_H12_P1_H12

value: 24h 0.5mM BSA


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo RNAseI, biol rep 1

description:
rpf_neg_1
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv


title: LZ_mNnN_05

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
C4

value: lymph node

value: Germinal Center LZ B cells


title: P0-M-HT2: P0-male-hetero replicate2

value: whole brain

value: male


title: WT-rep3

city: zhengzhou

first: Guo

last: Jia

address: 1 Jianshe Dong Lu, Erqi District,

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
The sequencing quality of the removed reads was evaluated by FASTQC software.The reference genome was compared by Hisat2 software
The Stringtie software was used to estimate the transcriptional abundance with reference to the annotation information of the official database
Using R software Ballgown, FPKM calculations at the gene level and transcription level were performed, and differences in gene level and transcriptional level expression were calculated, respectively, and differences between samples or groups were screened to express genes
PCA analysis, correlation analysis based on gene expression level, clustering of differential expression genes, GO functional significantity richness analysis, Pathway significant richness analysis
Genome_build: mm10
Supplementary_files_format_and_content: files include FPKM values for each Sample

source_name: Kidney foot process cells

growth_protocol: Cells are cultured using 1640 medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Cells were infected with lentivirus vectors that encoded either dlx6-os1 or an empty vector (control) according to the manufacturers’ instruction

value: Kidney


title: CNT_H11_P1_H11


title: LZ_mNnP_05

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
C3


title: K17040651_P1_H10

value: 24h 0.5mM 7(Z), 10(Z), 13(Z), 16(Z)-Docosatetraenoic Acid


title: DZ_mNnP_05

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
C2

value: Germinal Center DZ B cells


title: WT-rep2


title: K5plusK19plus replicate B

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

data_processing:
Raw reads for individual replicates were processed with HiC-Pro (v 2.11.4) and aligned to hg19.
Replicate samples for each cell type were quality controlled and checked for genome-wide signal correlation before merging with HiC-Pro.
Enriched regions representing H3K27ac peaks were detected using MACS2.
Chromatin loops were detected in each cell type-specific dataset using FitHiChIP v8.1 at 2 kb resolution limiting to 2 Mb interaction distance.
Peak-to-all loops were used for background modeling and a q < 0.01 threshold set to determine significant interactions.
Assembly: hg19
Supplementary files format and content: tab-delimited text file output from FitHiChIP including statistically significant chromatin interaction scores for each sample
Library strategy: Hi-ChIP

source_name: Breast

extract_protocol:
Cells were counted using the Countess II automated cell counter (Thermo Scientific) and fixed with 2% formaldehyde using the Arima HiC+ Kit (Arima, A101020). HiChIP libraries were generated with the Arima HiChIP kit using an antibody against H3K27ac (Active Motif AbFlex: 91193). 1e6 fixed cells were used in restriction enzyme digest, biotin end filling ligation reactions to the manufacturer’s protocol.
Libraries were prepared using the KAPA Kit (KAPA, KK2620), according to the Arima-HiC kit protocol. Libraries were indexed using the Swift Biosciences indexing kit then paired-end sequenced (150bp) with Illumina Novaseq 6000 to generate >500M raw reads per library.

value: Breast

value: Mammary epithelial


title: K562 CEBPA reporter cell line, nontargeting sgRNA ribo RNAseI, biol rep 3

description:
rpf_neg_3
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv

value: myeloid leukemia cells

value: RNAseI


title: K5plusK19plus replicate A


title: LZ_mNnN_04

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
B8


title: dlx6-os1 overexpression-rep3

value: dlx6-os1 overexpression


title: DZ_mNnN_05

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
C1

value: B1-8hi c-Myc-GFP


title: WT-rep1


title: CNT_H8_P1_H8

value: Mouse INsulinoma 6 (MIN6)


title: B80T5 replicate B


title: K67375056_P1_H7

value: 24h 0.5mM Dodecanoic acid


title: LZ_mNnP_04

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
B7


title: K5plusK19minus-replicate 2

data_processing:
Adapters trimmed using Cutadapt v1.13 and reads aligned to GRCh37 using Bowtie v2.2.9.
Peaks were called using MACS2 and cell type-specific replicating peaks identified using BedTools.
Assembly: hg19
Supplementary files format and content: Regions of open chromatin in narrowPeak format produced by MACS2

extract_protocol:
Profiling of regions of open chromatin using protocols reported in Buenrostro JD et al., ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 2015, 109:21 29 21-21 29 29.
Duplicate libraries were prepared for each cell type and paired-end sequenced (150bp) generating a minimum of 40M filtered reads per library.


title: K53322389_P1_H6

value: 24h 0.5mM 9(Z)-Tetradecenoic acid


title: SAH_3_3

city: Nanjing

first: Bin

last: Sheng

address: Zhongshan road 321

department: Department of Neurosurgery

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic
Supplementary files format and content: excel,expression profiles

source_name: blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
RNA libaries were prepared for sequencing using standard llumina protocols

tag: condition

value: subarachnoid hemorrhage blood

value: blood

tag: rna population

value: exosome microRNA

value: no


title: DZ_mNnP_04

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
B6

value: lymph node


title: CNT_H5_P1_H5

value: 24h 0.5mM BSA


title: K03070961_P1_H9

value: 24h 0.5mM 5(Z), 8(Z), 11(Z), 14(Z)-Eicosatetraenoic Acid


title: K5plusK19plus-replicate 2


title: DZ_mNnN_04

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
B5

value: Germinal Center DZ B cells


title: K5plusK19plus-replicate 1

value: Breast


title: dlx6-os1 overexpression-rep2

value: Kidney


title: B80T5 replicate A

value: Mammary epithelial


title: K32311524_P1_H3

value: 24h 0.5mM 5(Z), 8(Z)-Eicosadienoic acid


title: SAH_3_1


title: THP_1_P2_A5

value: 24h 0.001mM Thapsigargin


title: LZ_mNnP_03

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
B3

value: Germinal Center LZ B cells

value: B1-8hi c-Myc-GFP


title: HC_3

value: healthy control blood


title: K80340869_P1_H2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM Tetradecanoic acid


title: mesHMLE-replicate 2

value: mesHMLE


title: CNT_H1_P1_H1


title: HC_2

value: blood

value: exosome microRNA


title: mesHMLE-replicate 1


title: K5plusK19minus-replicate 1


title: PAOA_M_P1_G12

value: 24h 0.5mM Hexadecanoic acid and 9(Z)-Octadecenoic acid


title: SAH_3_2

value: subarachnoid hemorrhage blood

value: no


title: K46987408_P1_G11

value: 24h 0.5mM Heptadecanoic acid


title: LZ_mNnN_02

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
A8

value: lymph node


title: K63813237_P1_G10

value: 24h 0.5mM 10(Z)-Heptadecenoic acid


title: HMLE-replicate 2

value: Breast

value: HMLE

value: Mammary epithelial


title: LZ_mNnP_02

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
A7

value: Germinal Center LZ B cells


title: B80T5-replicate 2


title: K19189338_P1_G9

value: 24h 0.5mM 10-Undecenoic acid


title: DZ_mNnP_02

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
A6

value: Germinal Center DZ B cells

value: B1-8hi c-Myc-GFP


title: mesHMLE replicate 2

data_processing:
Raw data were aligned to Ensembl v70 gene models and hg19 coordinates with STAR v2.7.1a.
Duplicate reads were marked with PicardTools v2.19
Read counts mapping to transcriptome using featureCounts in subread v1.6.0
Count matrix generated using RSEM v1.3.1
Assembly: hg19
Supplementary files format and content: RSEM output ("genes.results") containing tab-delimited results of gene-level raw counts, TPM and FPKM values for each sample

extract_protocol:
RNA extraction was extracted using RNeasy kits (Qiagen) mRNA was enriched using polyT beads (Genewiz)
Sequencing libraries were prepared using Illumina strand-specific TruSeq kit.


title: mesHMLE replicate 1


title: dlx6-os1 overexpression-rep1

value: Kidney

value: dlx6-os1 overexpression


title: B80T17-replicate 2


title: B80T5-replicate 1


title: DZ_mNnN_02

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
A5


title: HC_1

value: healthy control blood

value: blood


title: K5plusK19plus replicate 1


title: B80T17-replicate 1


title: LZ_mNnN_03

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
B4


title: DZ_mNnP_03

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
B2


title: K43021856_P1_G7

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 10(Z),13(Z)-Nonadecadienoic acid


title: DZ_mNnN_03

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
B1


title: K5plusK19minus replicate 2


title: K38686876_P1_G6

value: 24h 0.5mM 14(Z)-Tricosenoic acid


title: LZ_mNnN_01

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnN_vs_LZ_mPnN.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
A4


title: LZ_mNnP_01

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
LZ_mNnP_vs_LZ_mNnN.xlsx
LZ_mNnP_vs_LZ_mPnN.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
A3


title: K5plusK19minus replicate 1


title: K5plusK19plus replicate 2


title: WT4

city: Jena

first: Leijie

address: Adolf-Reichwein-Straße 23

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
HISAT2
StringTie v2.2.1 (parameter-merge -F 0.1 -T 0.1)
gffcompare 0.12.6 (parameter- default)
Assembly: Version information of the reference genome is: Homo_sapiens.GRCh37_release87.genome.fa.
Supplementary files format and content: xlsx file include reads count and FPKM values for each Sample

source_name: Lung

growth_protocol: H441 cells were co-incubated with A. fumigatus conidia with MOI = 10 for 4 hours at 37°C and 5% (v/v) CO2.

extract_protocol:
RNA isolation from cells was performed using the Universal RNA purification Kit (Roboklon GmbH, Berlin, Germany)
Qualified RNA were processed for library construction. The procedures are described as follow: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: Lung

value: Epithelial

value: WT

value: incubation with A. fumigatus conidia for 4 hours


title: K15536865_P1_G4


title: THP_4_P1_G5

value: 24h 0.000001mM Thapsigargin


title: K75918321_P1_G3

value: 24h 0.5mM 9(E)-Octadecenoic acid


title: WT3


title: TUN_4_P1_G8

value: 24h 5ng/ml Tunicamycin


title: HMLE replicate 1

value: Breast

value: HMLE

value: Mammary epithelial


title: HMLE replicate 2


title: WT2


title: DZ_mNnP_01

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mNnN.xlsx
DZ_mNnP_vs_LZ_mNnP.xlsx
DZ_mNnP_vs_LZ_mPnN.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
A2

value: lymph node

value: Germinal Center DZ B cells

value: B1-8hi c-Myc-GFP


title: B80T5 replicate 2


title: HMLE-replicate 1


title: LZ_mPnP_05

description:
TPM_values.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
DZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mNnN_vs_LZ_mPnP.xlsx
LZ_mNnP_vs_LZ_mPnP.xlsx
LZ_mPnN_vs_LZ_mPnP.xlsx
F6

value: Germinal Center LZ B cells


title: K80325895_P1_G2

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 11(Z), 14(Z)-Eicosadienoic acid


title: B80T5 replicate 1


title: WT1


title: Ctr4

value: No treatment


title: B80T17 replicate 2


title: BCRM5215-2

city: Yinchuan

first: Jianwen

last: Wu

address: victory street

institute: Ningxia Medical University

description: 10x Genomics

data_processing:
Cell Ranger software (https://support.10xgenomics.com/single-cell-geneexpression/ software/overview/welcome) was used to perform data quality statistics on raw data and to match the reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
Mice PBMCs and spleen single cell suspension were extracted, and the dead cells were removed before sequencing
Cells from the spleen and PBMCs of infected (3 mice pooled) and uninfected (3 mice pooled) mice were washed once in PBS with 0.04% BSA and loaded to the 10X Genomics Chromium to capture single cells for scRNA-seq following the manufacturer's instructions of 10X Genomics Chromium Single-Cell 5' kit (V2.0). In brief, gel beads containing barcode information were combined with a mixture of cells and enzymes and then encapsulated by droplets of oil surfactant in a microfluidic "double-cross" system to form gel beads-in-emulsions (GEMs), which flowed into a reservoir and were collected. The gel beads were lysed to release the barcode sequence, cDNA fragments were reversed transcribed, and the sample was labeled. After breaking the gel beads and oil droplets, cDNA was broken into fragments of about 200-300 bp using enzymes, and sequencing connectors and primers were added. Finally, polymerase chain reaction (PCR) amplification was performed to obtain the DNA library. Libraries were sequenced on an Illumina NovaSeq 6000 (LC-Bio Technology Co. Ltd., HangZhou, China) sequencing system using a 150 bp paired-end multiplexing run.

value: spleen

tag: Sex

value: female

tag: disease state

value: Middle and late stage of infection

value: 6-8 weeks old

value: Echinococcus granulosus infection


title: BCRM5215-3

description: 10x Genomics

source_name: PBMCs

value: PBMCs

value: normal mice

value: PBS treatment


title: Ctr3

value: Lung

value: Epithelial

value: WT


title: K57135146_P2_B11

value: 24h 0.5mM 15(Z)-Tetracosenoic acid


title: CNT_F12_P1_F12

value: 24h 0.5mM BSA


title: CNT_G1_P1_G1


title: BCRM5215-1

description: 10x Genomics


title: Ctr2


title: BCRM5215-4

description: 10x Genomics


title: B80T17 replicate 1

value: Breast

value: Mammary epithelial


title: K91356052_P1_F11

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM 9(Z)-Hexadecenoic acid


title: DZ_mNnN_01

description:
TPM_values.xlsx
DZ_mNnN_vs_DZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mNnN.xlsx
DZ_mNnN_vs_LZ_mNnP.xlsx
DZ_mNnN_vs_LZ_mPnN.xlsx
DZ_mNnN_vs_LZ_mPnP.xlsx
A1

value: lymph node

value: Germinal Center DZ B cells

value: B1-8hi c-Myc-GFP


title: TCRM5215-4

description: 10x Genomics

value: spleen

value: female

value: 6-8 weeks old


title: MCF-7 cells treated with DMSO, dmso_4

city: Stockholm

first: Lars-Gunnar

last: Larsson

address: Solnavagen 9

department: Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institute

data_processing:
Demultiplexed .fastq files were aligned to the human GRCh37 reference genome using Tophat v 2.0. After alignment, .bam files from two separate flowcell lanes were merged using samtools. Raw read counts per gene were then generated using htseq-count v0.6.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: CSV file with raw read counts per gene per sample

source_name: Breast carcinoma cell line

extract_protocol: Libraries for RNA sequencing were prepared using the TruSeq Stranded Total RNA kit with RiboZero (Illumina) and sequenced on two lanes of the HiSeq 2500 platform with a single-end 1x51 setup and the HiSeq Rapid SBS v2 chemistry.

value: breast carcinoma cells

value: DMSO


title: TCRM5215-3

description: 10x Genomics

value: PBMCs

value: normal mice

value: PBS treatment


title: K43930766_P1_F9

value: 24h 0.5mM 11(E)-Eicosenoic acid


title: K57416915_P1_F10

value: 24h 0.5mM 6(E)-Octadecenoic acid


title: CAL51 cells

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing: STARsolo

source_name: breast

extract_protocol: ingle-cell transcriptomic of the 32 cell lines was performed by implementing in-house the DROP-seq technology. The microfluidics device for the generation of the droplet was fabricated using a bio-compatible, silicon-based polymer, polydimethylsiloxane (PDMS) that was rendered hydrophobic with Aquapel treatment as per protocol. In each sequencing experiment, cell suspension, bead suspension and carrier oil (QX200 droplet generation oil, Bio-Rad) were first loaded in syringes and then placed in syringe pumps (Leafluid). Flow rates of syringe pumps were set at 4,000 μL/h for both cell and barcoded bead suspensions while carrier oil syringe pump was set at 15,000 μL/h. In each sequencing experiment, cells and barcoded beads were, respectively, diluted at the concentration of 200 cell/μL in PBS with BSA 0.01% (Merck) and 120 bead/μL in lysis buffer. A self-built magnetic stirrer system was used to keep in suspension barcoded beads. To count the occurrence of a single cell together with a barcoded bead several tests were performed without lyses buffer in the bead suspension. In these tests, we observed about 5% of generated droplets filled with just one bead and one cell.

value: breast

value: triple negative breast cancer


title: MCF-7 cells treated with MYCMI-7, mycmi_2


title: TCRM5215-2

description: 10x Genomics

value: Middle and late stage of infection

value: Echinococcus granulosus infection


title: MDAMB468 cells


title: MCF-7 cells treated with DMSO, dmso_3


title: CNT_F8_P1_F8

value: Mouse INsulinoma 6 (MIN6)

value: 24h 0.5mM BSA


title: TCRM5215-1

description: 10x Genomics


title: K71795348_P1_F6

value: 24h 0.5mM 10(Z)-Nonadecenoic acid


title: K33396764_P1_F7

value: 24h 0.5mM 9(Z), 12(Z), 15(Z)-Octadecatrienoic Acid


title: KO3 input

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction:
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: bigwig files for each samples

source_name: ALKBH5flox/flox, αMyHC-Cre-DOX-3

growth_protocol: Myocardial tissues of ALKBH5-Control(WT, ALKBH5flox/flox) mice and ALKBH5 myocardial-specific knockout(KO, ALKBH5flox/flox, αMyHC-Cre) mice were methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Oiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR

treatment_protocol: Mice were intraperitoneally injected with 20mg/kg doxorubicin.

value: Heart

tag: rip antibody

value: input

value: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-3

value: Doxorubicin