title: BMDMs treated with conditioned medium from IL1b-treated enteric glia (24h) for 3h rep 4

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

country: Germany

institute: University Clinics Bonn

description:
primary BMDMs
BMDMs treated with conditioned medium from IL1b-treated enteric glia (24h) for 3h

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Alignment STAR - 2.5.3a - Version 10.0.21.1116
Partek Flow Software - Post-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Assembly: mm10 Ensembl Transcripts release 99

source_name: bone-marrow

extract_protocol:
Qiagen RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with the indcated substances or media.

tag: fraction

value: Total RNA (input)


title: C49_wt

status: Public on Jul 11 2022

type: SRA

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description: mRNA

library_source: transcriptomic

data_processing:
Reads were mapped to the mm10 mouse genome using STAR v2.7.0a with default settings.
Reads per gene was computed using rpkmforgenes.py with default settings and NCBI RefSeq annotation with addition of the mCherry cDNA sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: data.counts_geo.csv: Comma-separated text file containing number of mapped reads per gene for all samples.

molecule: total RNA

organism: Mus musculus

source_name: Adult mouse midbrain

extract_protocol:
FACS
Smart-seq2

tag: tissue

value: Adult mouse midbrain

tag: cell type

value: mDA

tag: strain

value: DatCreEed

tag: genotype

value: wt

tag: sequencing batch

tag: timepoint

value: 8 months

tag: biological replicate

tag: Sex

value: Male


title: BMDMs treated with conditioned medium from IL1b-treated enteric glia (24h) for 3h rep 2

tag: treatment


title: BMDMs treated with conditioned medium from IL1b-treated enteric glia (24h) for 3h rep 3


title: blood, Day 0, UGA4, 311

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

country: USA

institute: National Institutes of Health

data_processing:
Trim Galore! v0.6.6
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!
STAR v2.6.1d
Trimmed sequence reads were mapped to GRCh38.p10 using STAR (parameters- quantMode: TranscriptomeSAM twopassMode: Basic runRNGseed: 0 outFilterMultimapNmax: 20 alignSJDBoverhangMin: 1 outSAMattributes: NH HI AS NM MD quantTranscriptomeBan: Singleend)
Salmon v1.4.0
Aligned reads were used to perform transcript quantification using salmon quant in alignment-based mode (parameters - libType: IU)
Assembly: hg38
Supplementary files format and content: comma-separated value tables contain transcripts-per-million for each sample

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from each blood sample in randomized batches using the PAXgene Blood miRNA Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations and stored at -80°C in a LoBind twin.tec 96-well PCR plate (Eppendorf, Hamburg, Germany). All samples were quantified with the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and their fragment size distribution was measured with an RNA Screentape on a 4200 TapeStation System (Agilent, Santa Clara, CA)
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the manufacturer’s protocols using either 1ug of input RNA or, in the case of several low-yield samples, the maximum possible input mass. AMPure XP Beads (Beckman Coulter, Brea, CA) were used in place of the supplied NEBNext Sample Purification Beads. Libraries were prepared in 3 batches with two negative library prep controls in each batch to monitor for reagent or sample-to-sample contamination. Each library was barcoded with NEBNext Multiplex Oligos for Illumina (NEB, Ipswich, MA) in a rotating scheme, which ensured that each pool had a unique set of barcodes. Each library was quantified with the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent, Santa Clara, CA) on a 4200 TapeStation System. All libraries made from experimental samples were of sufficient molarity for pooling and sequencing.
A single sequencing library was prepared from a single biological sample. Libraries were then pooled with equimolar input at either 2nM or 3nM into sets of 96 libraries for RNA sequencing on a NovaSeq 6000 with the S1 2x150 - 300 Cycle configuration (Illumina, San Diego, CA) at the Genomics Core Facility (Center for Genomics and Systems Biology, New York University).

value: Whole Blood

tag: time

value: Day 0


title: blood, Day 0, UGA4, 124


title: C47_wt

description: mRNA


title: blood, Day 0, UGA4, 125


title: blood, Day 0, UGA4, 135


title: C45_wt

description: mRNA

value: Female


title: blood, Day 0, UGA4, 148


title: small RNA_hypothalamus, CG pig, rep3

city: Rongchang

first: Renli

last: Qi

address: Changlong Road 51#

country: China

institute: Chongqing Academy of Animal Science

description:
small RNA
FMT_3

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: Sus scrofa 11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

source_name: hypothalamus

extract_protocol:
Total RNA from the hypothalamus was extracted using TRIzol (Invitrogen, USA).5.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq transcriptome strand librariy was prepared following TruSeqTM stranded total RNA Kit   from Illumina (San Diego, CA)

treatment_protocol:
Six newborn GF piglets were obtained via hysterectomy from a multiparous Chinese Bama sow.
Three of them were introduced to gut microorganisms through the faecal microbiota transplant (FMT) method for colonization (CG piglets)from day 3 to day 7 after born.

value: hypothalamus

value: with gut microbiota

value: male

tag: developmental stage

value: 45 days old


title: small RNA_hypothalamus, CG pig, rep2

description:
small RNA
FMT_2


title: BMDMs treated with conditioned medium from IL1b-treated enteric glia (24h) for 3h rep 1


title: blood, Day 0, UGA4, 304


title: small RNA_hypothalamus, CG pig, rep1

description:
small RNA
FMT_1


title: BMDMs treated with conditioned medium from enteric glia (24h) for 3h rep 4

description:
primary BMDMs
BMDMs treated with conditioned medium from enteric glia (24h) for 3h

value: CM-veh


title: blood, Day 0, UGA4, 146


title: blood, Day 0, UGA4, 185


title: MYCER_24h_1

city: Farmington

first: Olga

last: Anczukow

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Read filtering and cropping of reads to same length using Trimmomatic (v0.39)
mapping of reads to Gencode GRCh38 v.32 reference transcript annotation using STAR in 2-pass mode (v2.7.3a)
Transcript assembly and quantification with Stringtie (v2.1.3b)
Differential splicing using rMATS (v4.1.0)
Genome_build: GRCh38 v .32
Supplementary_files_format_and_content: gene_count_matrix

source_name: human mammary epithelial cells

growth_protocol: For 3D culture assays, MCF-10A and MCF-10A MYC-ER cells were seeded at a density of 10,000 cells per well in triplicate on a 4-well glass chamber slide coated with Matrigel Growth Factor Reduced (BD Biosciences) as described (Debnath et al., 2003; Liberzon et al., 2015). Media was replaced at 72h.

extract_protocol:
Cells were washed with PBS (1X) and the Matrigel was dissolved by incubating slides at 4°C in Cell Recovery Solution (BD Biosciences). Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.
Barcoded RNA libraries were prepared starting with 1ug for MCF-10A of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).
Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina HiSeq, equal amounts of 3 libraries were pooled per lane.

treatment_protocol: Starting on day 3, cells were treated with 1μM 4-hydroxy tamoxifen (4-OHT) (Sigma) for 48h, 24h, 8h, or 0h, prior to collection. All samples were collected at the same time on day 5.

tag: cell line

value: 4OHT 24h


title: blood, Day 0, UGA4, 290


title: small RNA_hypothalamus, GF pig, rep3

description:
small RNA
GF_3

value: without gut microbiota


title: dat_8mo_D835_wt_K9

library_source: genomic

data_processing:
Reads were mapped to the mm10 mouse genome using bowtie2 v2.3.5.1 with default settings.
Duplicate reads were marked using Picard tools v2.10.3.
Biological replicates were pooled using samtools.
Coverage of pooled samples were generated with deepTools v 3.1 using the bamCoverage function. Counts were transformed to RPKMs, binsize was set to 50bp, and duplicates were ignored.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of coverage.

molecule: genomic DNA

extract_protocol:
Midbrain dopamine producing neurons (mDA) from DATcre-Eed-Rpl10a-mCherry mice were extracted. Tissue was thawed and dissociated using a 1 mL dounce homogenizer (Wheaton) in ice-cold lysis buffer (0.32M sucrose, 5mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT, 1x complete proteinase inhibitor, EDTA-free (Roche)). The homogenate was layered over a sucrose cushion (1.8M sucrose, 3mM MgAc, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) before centrifugation for 2.2h at 30.000g in a Beckman J-25 centrifuge using a J13.1 rotor. The pelleted nuclei were re-suspended in a nuclear storage buffer (15% sucrose, 10 mM Tris_HCl, pH 7.2, 70 mM KCl, 2 mM MgCl2) supplemented with RNAse inhibitor (RNAse out, Invitrogen) and proteinase inhibitor (Complete, Roche). Re-suspended nuclei were passed through a 30 μm cup filcon (BD Biosciences, 340625) into a BSA-coated tube for sorting. FACS was performed using a FACSAria cell sorter and the FACSDiva software (BD Biosciences). The nuclei were identified by forward and side scatter gating and a 633 nm laser with a 660/20 or 616/23 filter. A 100 μm nozzle, sheath pressure of 20–25 psi, and an acquisition rate of up to 1000 events per second were used. Cell-type specific nuclei were collected in batches of 1000, supplemented with a nuclear buffer (10 mM Tris (pH 8.0), 100 mM NaCl, 2 mM MgCl2, 0.3M Sucrose, 0.25% IGEPAL CA-630) to a total volume of 10 uL and subsequently snap frozen on dry ice for later use. ChIP and library generation for ChIP-seq was performed using the previously described ULI-NChIP protocol [20] with minor modifications. Briefly, one batch of 1000 nuclei per animal and antibody was thawed on ice and fragmented for 10 min using MNase at 21 °C and diluted in NChIP immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 15 mM NaCl, 0.1% Triton X-100, 1x EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride (PMSF, Sigma, P7626)). Chromatin was pre-cleared with 5 μl of a 1:1 mixture of Protein A and Protein G Dynabeads (Life Technologies, 10006D and 10007D) and IPed over night at 4 °C with 0.25 of anti-H3K9me3 (Active Motif, 39161), anti-H3K27me3 (Cell Signaling, 9733) or anti-H3K4me3 (Cell Signaling, 9751). Beads were washed twice with 400 μl of a buffer containing 20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 2 mM EDTA and 150 mM NaCl and twice with a buffer containing 20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 2 mM EDTA and 500 mM NaCl. Protein–DNA complexes were eluted in 30 μl of a ChIP elution buffer containing 100 mM NaHCO3 and 1% SDS for 2 h at 68 °C. The eluted chromatin was purified by phenol chloroform, precipitated with EtOH and re-suspended in 10 mM Tris-HCl pH 8.0.
To generate libraries for sequencing, ChIPed DNA was end-repaired in a mixture of dNTP (NEB, N0447L), T4 DNA polymerase (NEB, M0203L), Klenow DNA polymerase (NEB, M0210L) and T4 PNK (NEB, M0201L) in T4 DNA ligase buffer (NEB, B0202S) for 30 min at room temperature. The product was purified with 1.8x Agencourt AMPure XP beads (Beckman Coulter, A63881) and then poly-A tailed in dATP (NEB, N0440S) and Klenow (3’-5’ exo-) (NEB, M0212L) in NEB buffer 2 (NEB, B7002S) at 37 °C for 30 min followed by another 1.8x AMPure bead purification step. The product was ligated to NEBnext adaptors for Illumina (NEB, E7337A) with Quick DNA ligase (NEB, M2200L) in 2x Quick DNA ligation buffer at room temperature for 1-2h, trimmed with USER enzyme (NEB, E7338A) at 37 °C for 15 min and subsequently purified with 0.8x AMPure beads. The adapter-ligated ChIP-DNA was then PCR-amplified using 2x Phusion HF Master mix (NEB, M0531L) and NEBNext Multiplex Oligos for Illumina, Index Primers Set 1 (NEB, E7335L). The final libraries were cleaned up using 0.8x AMPure beads, quantified on a Qubit 3.0 Fluorometer (ThermoFisher) and quality checked on a 2100 Bioanalyzer system (Agilent) using High Sensitivity DNA kit (Agilent, 5067-4626).

value: PRC2 wt

tag: chip antibody

value: H3K9me3 (Active Motif, 39161)

value: M


title: BMDMs treated with conditioned medium from enteric glia (24h) for 3h rep 3

value: Total RNA (input)


title: dat_8mo_D835_wt_K4

value: Adult mouse midbrain

value: mDA

value: DatCreEed

value: H3K4me3 (Cell Signaling, 9751)


title: BMDMs treated with conditioned medium from enteric glia (24h) for 3h rep 2


title: blood, Day 0, UGA4, 118

value: Whole Blood

value: Day 0


title: BMDMs treated with conditioned medium from enteric glia (24h) for 3h rep 1


title: small RNA_hypothalamus, GF pig, rep2

description:
small RNA
GF_2

value: hypothalamus


title: small RNA_hypothalamus, GF pig, rep1

description:
small RNA
GF_1


title: BMDMs treated with RPMI medium for 3h rep 4

description:
primary BMDMs
BMDMs treated with RPMI medium for 3h

value: Control (RPMI)


title: blood, Day 0, UGA4, 149


title: dat_8mo_D834_wt_K9

value: 8 months


title: dat_8mo_D835_wt_input


title: dat_8mo_D835_wt_K27

value: H3K27me3 (Cell Signaling, 9733)


title: dat_8mo_D834_wt_input


title: blood, Day 0, UGA4, 14


title: BMDMs treated with RPMI medium for 3h rep 3


title: hypothalamus, CG pig, rep3

description:
Long RNA
FMT_3

value: with gut microbiota

value: male

value: 45 days old


title: hypothalamus, CG pig, rep2

description:
Long RNA
FMT_2


title: blood, Day 0, UGA4, 253


title: hypothalamus, CG pig, rep1

description:
Long RNA
FMT_1


title: dat_8mo_D834_wt_K4

value: PRC2 wt


title: blood, Day 0, UGA4, 208


title: Liver, normal, N30

city: Chengdu

first: Kui

last: Wang

address: No.17, Section 3, South Renmin Rd

institute: Sichuan University

data_processing:
Illumina Casava1.7 software is used for basecalling.
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm8
Supplementary files format and content: Tab-delimited text files incculde PRKM values for each sample.

source_name: Liver

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.   In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: Liver

tag: disease state

value: Normal


title: BMDMs treated with RPMI medium for 3h rep 2

value: Total RNA (input)


title: hypothalamus, GF pig, rep3

description:
Long RNA
GF_3

value: without gut microbiota


title: glia + IL1b for 24h rep 2

description:
primary enteric glia
glia + IL1b for 24h

source_name: Small bowel muscularis externa


title: BMDMs treated with RPMI medium for 3h rep 1


title: blood, Day 0, UGA4, 209


title: dat_8mo_D834_wt_K27

value: Adult mouse midbrain

value: mDA

value: M


title: dat_8mo_D833_wt_input

value: DatCreEed

value: F


title: Liver, normal, N27


title: dat_8mo_D833_wt_K9

value: H3K9me3 (Active Motif, 39161)


title: dat_8mo_D833_wt_K4

value: H3K4me3 (Cell Signaling, 9751)


title: dat_8mo_D833_wt_K27

value: 8 months


title: glia + IL1b for 24h rep 1


title: glia control rep 3

description:
primary enteric glia
glia control

value: Control


title: Liver, normal, N28


title: hypothalamus, GF pig, rep1

description:
Long RNA
GF_1

value: hypothalamus


title: glia control rep 1

description:
primary enteric glia
glia control


title: Pediatric Nodal marginal zone lymphoma 55-1

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software 9.0
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: Inguinal LN

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: type of sample

value: Pediatric Nodal marginal zone lymphoma

tag: gender

value: male

value: FFPE


title: Liver, normal, N26

value: Liver


title: Pediatric Nodal marginal zone lymphoma 55-3

label_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602


title: glia control rep 2

description:
primary enteric glia
glia control

tag: fraction


title: dat_8mo_C250_wt_input

tag: tissue

value: PRC2 wt


title: Pediatric Nodal marginal zone lymphoma 53

source_name: neck


title: dat_8mo_C250_wt_K9

tag: cell type


title: glia + IL1b for 24h rep 3

value: Total RNA (input)


title: control 5 Progressive transformation of germinal centers

source_name: unknown

value: female


title: dat_8mo_C250_wt_K4

value: Adult mouse midbrain

tag: strain


title: Pediatric Nodal marginal zone lymphoma 54


title: hypothalamus, GF pig, rep2

description:
Long RNA
GF_2

value: without gut microbiota

value: 45 days old


title: control 4 Atypical Margina zone hyperplasia

value: Atypical Margina zone hyperplasia


title: Pediatric Nodal marginal zone lymphoma 52


title: control 2 Marginal zone hyperplasia

source_name: Cervical LN

value: Marginal zone hyperplasia


title: dat_8mo_C250_wt_K27

value: mDA

value: DatCreEed

tag: genotype

value: H3K27me3 (Cell Signaling, 9733)

value: F


title: Liver, normal, N24

value: Normal


title: Liver, normal, N25


title: Liver, normal, N23


title: dat_8mo_D263_mut_input

value: PRC2 mutant

value: 8 months

value: M


title: Liver, normal, N22

value: Liver


title: Liver, normal, N20


title: Liver, normal, N21


title: Pediatric Nodal marginal zone lymphoma 49

value: Pediatric Nodal marginal zone lymphoma

value: male

value: FFPE


title: Pediatric Nodal marginal zone lymphoma 50


title: Liver, normal, N19


title: dat_8mo_D263_mut_K9

value: Adult mouse midbrain

value: H3K9me3 (Active Motif, 39161)


title: dat_8mo_D263_mut_K4

value: H3K4me3 (Cell Signaling, 9751)


title: Hela, treated with DMSO, input chromatin

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description: inputDMSO

data_processing:
Final processed data obtained from sans spike-in quantitative ChIP-seq (siQ-ChIP) pipeline. Full codes at github via github.com/BradleyDickson/siQ-ChIP
IP and input data were aligned to genome, quantitative scale was computed from sample masses, fragment lengths, etc, and the siQ-scaled process track is alpha * IP/input
Assembly: hg38
Supplementary files format and content: bigwig files are quantitative siQ-ChIP tracks
Supplementary files format and content: All siQ-ChIP parameters are stored in a file called parameters.tgz

source_name: cervical

growth_protocol: HeLa cells (ATCC #CCL-2) were maintained in DMEM (Gibco, 11965092) supplemented with 10% FBS (Sigma, F0926) and 1% penicillin-streptomycin (Gibco, 15140122) and were grown in 37 degC with 5% CO \textsubscript{2}. Cells were passaged and plated 1 d before drug treatment. Media was then removed and replaced for drug treatment with 10 uM CBP30 (Cayman #14469 Batch: 0473336-73), 10 uM A485 (Cayman \#24119 Batch: 0581192-13), or vehicle dimethyl sulfoxide (DMSO) (Sigma 472301, Lot: SHBK2080). DMSO was volume matched for experiments and was either at 0.1\% or 0.02\% total volume. Cells were treated for 16 h and were then fixed and collected using the protocol described herein.

extract_protocol:
Cells were then lysed under hypotonic conditions in 1 mL of 20 mM Tris-HCl pH 8, 85 mM KCl, 0.5% NP- 40 (1 tablet of protease inhibitor (Roche, 11836170001) per 5 mL of buffer) for 30 min on ice. Nuclei (and other insoluble material) were collected by centrifugation at 1300 x g for 5 min at 4 degC, lysed by resuspension in 150 uL 50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS (1 tablet of protease inhibitor per 5 mL of buffer), and passaged five times through a 27-gauge needle (BD #309623 Lot: 0227218). Lysate was then diluted to 500 uL by addition of 350 uL of binding buffer (25 mM HEPES pH 7.5, 100 mM NaCl, 0.1% NP-40).  Five uL of RNAse A/T1 (Thermo Scientific, EN0551) was added, and the sample was incubated at 37 degC for 25 min. Next, CaCl\textsubscript{2} was added to a final concentration of 40 mM (21 uL of 1 M) followed by the addition of 75 U (3 uL of 25 U/uL) of micrococcal nuclease (MNase, Worthington Biochemical) and incubated at 37 degC for 5 min. MNase was quenched by the addition of 40 mM EDTA (46 uL of 500 mM EDTA), and the total volume was brought to 1 mL by the addition of 425 uL of binding buffer. Next, insolubilities were removed by centrifugation at max speed (about 21,000 x g) at 4 degC for 5 min, and the supernatant containing soluble chromatin was collected.
Library preparation was done using KAPA HyperPrep Kit (Roche, KK8504) with 4 uL of Illumina adapters (IDT, UDI) and sequenced on Illumina NextSeq 500 with a Mid-Output (paired-end 75 bp reads) flow cell. Input libraries had between 83-102M reads, and each IP library had 27-46M reads that passed QC, with 88% of the bases having quality scores >= 30.

value: cervical

value: HeLa

value: DMSO


title: Pediatric Nodal marginal zone lymphoma 48

source_name: Postauricular, right


title: Hela, treated with CBP30, input chromatin

treatment_protocol: HeLa cells (ATCC #CCL-2) were maintained in DMEM (Gibco, 11965092) supplemented with 10% FBS (Sigma, F0926) and 1% penicillin-streptomycin (Gibco, 15140122) and were grown in 37 degC with 5% CO \textsubscript{2}. Cells were passaged and plated 1 d before drug treatment. Media was then removed and replaced for drug treatment with 10 uM CBP30 (Cayman #14469 Batch: 0473336-73), 10 uM A485 (Cayman \#24119 Batch: 0581192-13), or vehicle dimethyl sulfoxide (DMSO) (Sigma 472301, Lot: SHBK2080). DMSO was volume matched for experiments and was either at 0.1\% or 0.02\% total volume. Cells were treated for 16 h and were then fixed and collected using the protocol described herein.

value: p300 inhibitor CBP30


title: Hela, treated with A485, input chromatin

value: p300 inhibitor A485


title: Liver, normal, N18


title: dat_8mo_D263_mut_K27

value: mDA

value: DatCreEed

value: H3K27me3 (Cell Signaling, 9733)


title: Pediatric Nodal marginal zone lymphoma 47

source_name: neck left


title: Liver, normal, N17

value: Normal


title: Pediatric Nodal marginal zone lymphoma 46


title: dat_8mo_C251_mut_input

value: PRC2 mutant

value: 8 months

value: F


title: Pediatric Nodal marginal zone lymphoma 44

source_name: Groin, right

value: Pediatric Nodal marginal zone lymphoma

value: male


title: Pediatric Nodal marginal zone lymphoma 43

source_name: supraclavicular

value: FFPE


title: Pediatric Nodal marginal zone lymphoma 42

source_name: neck right


title: HeLa, treated with DMSO, IP for H3K27ac

value: vehicle DMSO


title: Pediatric Nodal marginal zone lymphoma 41


title: dat_8mo_C232_mut_K9

value: Adult mouse midbrain

value: H3K9me3 (Active Motif, 39161)


title: Pediatric Nodal marginal zone lymphoma 40


title: Pediatric Nodal marginal zone lymphoma 45


title: dat_8mo_C232_mut_K4

value: H3K4me3 (Cell Signaling, 9751)


title: dat_8mo_C232_mut_K27


title: dat_8mo_C251_mut_K4


title: dat_8mo_C251_mut_K27


title: HeLa, treated with CBP30, IP for H3K18ac

value: cervical

value: HeLa


title: dat_8mo_C251_mut_K9


title: HeLa, treated with A485, IP for H3K27ac

value: p300 inhibitor A485


title: dat_8mo_C232_mut_input

value: mDA


title: HeLa, treated with CBP30, IP for H3K27ac

value: p300 inhibitor CBP30


title: HeLa, treated with DMSO, IP for H3K18ac


title: Liver, normal, N15

value: Liver


title: Liver, normal, N16

value: Normal


title: Liver, normal, N13


title: Liver, normal, N12


title: Pediatric Nodal marginal zone lymphoma 39

source_name: submental/neck


title: dat_8mo_C216_mut_input

source_name: Adult mouse midbrain

value: DatCreEed

value: PRC2 mutant

value: M


title: Liver, normal, N10


title: IMSA091_H

city: Boston

last: Ginebaugh

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
PBMC_counts.csv
IMSA_PBMC_normandbatchcorrected.csv

data_processing:
Quality control for raw FASTQ files was performed using FastQC, and the lowquality reads and 3’ adapters were trimmed with Trim Galore! (Babraham Bioinformatics, Cambridge, United Kingdom)
The RNA sequence aligner STAR was used to align the trimmed reads to the reference human genome (hg38)
Gene expression was quantified  from mapped genes using featureCounts
Quantified gene expression was normalized using the vst package from DESeq2
Samples were controlled for batch effect using the COMBAT algorithm
Assembly: hg38
Supplementary files format and content: csv includes raw counts or normalized/batch corrected counts for each sample

source_name: PBMC

extract_protocol:
Frozen RNA samples were purified removing DNA and rRNA with standard procedures.
cDNA libraries were prepared for sequencing using Illumina protocols. (Illumina Document #1000000040499v00 and Illumina Kit #20020596).

value: PBMC

tag: age screened

value: H

tag: batch

tag: condition

value: healthy

tag: subject id


title: HeLa, treated with A485, IP for H3K18ac

tag: treatment


title: Liver, normal, N11


title: IMSA093_H

tag: Sex

value: male


title: Liver, normal, N9


title: IMSA090_H

value: female


title: IMSA094_S

value: S

value: ast


title: Liver, normal, N8


title: dat_8mo_C216_mut_K9

value: Adult mouse midbrain

value: H3K9me3 (Active Motif, 39161)

tag: timepoint

value: 8 months

tag: biological replicate


title: Pediatric Nodal marginal zone lymphoma 38

source_name: submental

value: Pediatric Nodal marginal zone lymphoma

value: FFPE


title: IMSA087_S


title: Pediatric Nodal marginal zone lymphoma 37

source_name: inguinal, right


title: dat_8mo_C216_mut_K4

value: mDA

tag: chip antibody

value: H3K4me3 (Cell Signaling, 9751)


title: Liver, normal, N7

source_name: Liver

value: Liver

tag: disease state

value: Normal


title: Pediatric Nodal marginal zone lymphoma 35

source_name: axilla

tag: type of sample


title: IMSA086_H


title: Pediatric Nodal marginal zone lymphoma 36

tag: gender


title: Liver, normal, N6


title: Liver, normal, N1


title: Pediatric Nodal marginal zone lymphoma 32

source_name: cervical right LN


title: Pediatric Nodal marginal zone lymphoma 34

source_name: left neck


title: IMSA080_S


title: Pediatric Nodal marginal zone lymphoma 33

source_name: cervical left LN


title: IMSA083_H


title: Liver, normal, N5


title: Liver, normal, N4


title: dat_4mo_D300_wt_K9

value: DatCreEed

value: PRC2 wt

value: 4 months

value: F


title: IMSA069_H

value: PBMC

value: H

value: healthy


title: dat_8mo_C216_mut_K27

value: PRC2 mutant

value: H3K27me3 (Cell Signaling, 9733)

value: M


title: dat_4mo_D300_wt_K4

value: Adult mouse midbrain


title: Liver, normal, N3


title: dat_4mo_D300_wt_K27


title: dat_4mo_D300_wt_input


title: IMSA067_S

value: female

value: S

value: ast


title: Liver, tumor, T28

value: Tumor


title: IMSA068_S


title: Pediatric Nodal marginal zone lymphoma 29

source_name: submandibular lymph node

value: Pediatric Nodal marginal zone lymphoma

value: male

value: FFPE


title: dat_4mo_D296_wt_K9

value: mDA

value: DatCreEed

value: PRC2 wt

value: H3K9me3 (Active Motif, 39161)


title: IMSA085_H

value: PBMC

value: H


title: Pediatric Nodal marginal zone lymphoma 31

source_name: parotid


title: Pediatric Nodal marginal zone lymphoma 28

source_name: inguinal left


title: IMSA065_S


title: dat_4mo_D296_wt_K4

value: H3K4me3 (Cell Signaling, 9751)

value: 4 months


title: IMSA062_S


title: Liver, tumor, T30

value: Liver


title: Pediatric Nodal marginal zone lymphoma 27

source_name: cervical


title: dat_4mo_D295_wt_input

value: Adult mouse midbrain

value: M


title: Liver, tumor, T25


title: dat_4mo_D296_wt_input


title: Liver, tumor, T24


title: IMSA059_S

value: S


title: dat_4mo_D296_wt_K27

value: H3K27me3 (Cell Signaling, 9733)


title: Liver, tumor, T26

value: Tumor


title: Pediatric Nodal marginal zone lymphoma 23

source_name: right neck

value: Pediatric Nodal marginal zone lymphoma


title: IMSA061_M

value: female

value: ast


title: dat_4mo_D295_wt_K27

value: mDA


title: Liver, tumor, T27


title: IMSA057_M


title: Pediatric Nodal marginal zone lymphoma 25

value: male

value: FFPE


title: Pediatric Nodal marginal zone lymphoma 19


title: Liver, tumor, T23


title: IMSA058_M


title: Pediatric Nodal marginal zone lymphoma 17


title: Pediatric Nodal marginal zone lymphoma 16


title: IMSA064_H

value: healthy


title: Liver, tumor, T22


title: Liver, tumor, T21


title: Liver, tumor, T20


title: dat_4mo_D295_wt_K9

value: DatCreEed

value: PRC2 wt

value: H3K9me3 (Active Motif, 39161)


title: IMSA056_M

value: PBMC


title: IMSA055_S


title: dat_4mo_D294_wt_K9

value: 4 months


title: dat_4mo_D294_wt_input

value: Adult mouse midbrain


title: Liver, tumor, T19

value: Liver


title: dat_4mo_D295_wt_K4

value: H3K4me3 (Cell Signaling, 9751)

value: M


title: Pediatric Nodal marginal zone lymphoma 14

source_name: inguinal


title: dat_4mo_D294_wt_K4


title: Pediatric Nodal marginal zone lymphoma 12

source_name: scalp


title: Pediatric Nodal marginal zone lymphoma 13

source_name: neck


title: Liver, tumor, T18

value: Tumor


title: IMSA054_S

value: S


title: IMSA052_H

value: female

value: H


title: dat_4mo_D294_wt_K27

source_name: Adult mouse midbrain

value: mDA

value: H3K27me3 (Cell Signaling, 9733)


title: Liver, tumor, T16


title: Liver, tumor, T17


title: dat_4mo_D226_mut_input

value: PRC2 mutant

value: F


title: IMSA050_M

source_name: PBMC

value: male

value: ast


title: Pediatric Nodal marginal zone lymphoma 11

source_name: right inguinal

value: Pediatric Nodal marginal zone lymphoma

value: FFPE


title: Pediatric Nodal marginal zone lymphoma 10

source_name: Inguinal LN


title: IMSA049_H

value: PBMC

value: healthy


title: Liver, tumor, T15

source_name: Liver

value: Liver


title: Pediatric Nodal marginal zone lymphoma 15

source_name: submental


title: dat_4mo_D226_mut_K9

value: Adult mouse midbrain

value: DatCreEed

value: H3K9me3 (Active Motif, 39161)

value: 4 months


title: IMSA048_S

value: female

value: S


title: Pediatric Nodal marginal zone lymphoma 9


title: Liver, tumor, T13

value: Tumor


title: Pediatric Nodal marginal zone lymphoma 8


title: IMSA046_M

value: M


title: dat_4mo_D226_mut_K27

value: mDA

value: PRC2 mutant

value: H3K27me3 (Cell Signaling, 9733)


title: IMSA045_S

value: male

value: ast


title: Liver, tumor, T10


title: Liver, tumor, T11


title: Pediatric Nodal marginal zone lymphoma 7

value: Pediatric Nodal marginal zone lymphoma

value: FFPE


title: dat_4mo_D192_mut_input

value: F


title: Pediatric Nodal marginal zone lymphoma 6

source_name: posterior neck


title: dat_4mo_D192_mut_K9


title: IMSA041_M

value: PBMC


title: Liver, tumor, T9

value: Liver


title: Pediatric Nodal marginal zone lymphoma 5

source_name: occiput


title: dat_4mo_D192_mut_K4

value: Adult mouse midbrain

value: DatCreEed

value: H3K4me3 (Cell Signaling, 9751)


title: IMSA040_M


title: Liver, tumor, T7


title: Liver, tumor, T8


title: Liver, tumor, T12


title: IMSA039_S


title: dat_4mo_D226_mut_K4

value: 4 months


title: Pediatric Nodal marginal zone lymphoma 4

source_name: submandibular


title: dat_4mo_D187_mut_input


title: Liver, tumor, T6


title: dat_4mo_D187_mut_K9

value: H3K9me3 (Active Motif, 39161)


title: Pediatric Nodal marginal zone lymphoma 3


title: IMSA038_M

value: female


title: IMSA037_S

value: S


title: dat_4mo_D187_mut_K4

value: mDA


title: Liver, tumor, T5

value: Tumor


title: Pediatric Nodal marginal zone lymphoma 2


title: Pediatric Nodal marginal zone lymphoma 1

source_name: preauricular LN


title: dat_4mo_D187_mut_K27

value: PRC2 mutant

value: H3K27me3 (Cell Signaling, 9733)


title: IMSA044_S

value: ast


title: IMSA036_M

value: M


title: dat_4mo_D192_mut_K27


title: Liver, tumor, T4


title: Pt2CB

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
The single nuclei RNA sequencing data were demultiplexed and aligned using Cell Ranger software (version 4.0.0, 10X Genomics, Pleasanton, CA). Reads were aligned to the human genome GRCh38 version 101 with the following modifications: 1. Human genome files GRCh38 were downloaded from Ensembl; 2. the “transcript” lines in the .gtf file were converted into “exon” lines without changings to the remaining; 3. The reference files were generated using the cellranger “mkref” function; 4. Reads were aligned to the modified file and counted using cellranger “count” function with the chemistry option specified as “SC3Pv3”.
Assembly: GRCh38
Supplementary files format and content: Gene count matrix of cells from each tissue in .csv format

source_name: Ciliary body

extract_protocol:
Dissected tissues were flash frozen on dry ice and stored at -80 deg C until processing. Frozen tissue samples were homogenized in a dounce homogenizer with NP-40 based lysis buffer and strained to remove debris. The nuclei were isolated by centrifugation and flow cytometry sorting with DAPI staining. The sorted nuclei were resuspended in 0.04% non-acetylated BSA in PBS to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 10,000 cells.
Single nuclei libraries were generated with Chromium 3’ v3 or v3.1 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Single nuclei were partitioned into Gel beads in EMulsion (GEMs), where nuclei were lysed and mRNA was barcoded in reverse transcription. The cDNA was amplified, sheared, and attached to a 5’ adaptor and sample index barcode. On average, 7,000-10,000 single nuclei were loaded on each channel and 4,000-6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500 or NovaSeq.
Chromium 3’ v3 or v3.1 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Eyes were enucleated from human donors with no clinical history of ocular disease or surgery within 2-4 hours after death. The eyes were transported on ice to the laboratory in a humid chamber for further dissection and processing.

tag: site

value: Ciliary body

value: Left Eye

tag: donor

tag: 10x kit version


title: IMSA035_S

tag: tissue

value: PBMC

tag: cell type


title: Hu220OSCSWS2

source_name: Cornea sclera wedge

value: Cornea sclera wedge


title: Liver, tumor, T1

value: Liver


title: dat_4mo_D186_mut_K9

value: Adult mouse midbrain

tag: strain

value: DatCreEed

tag: genotype

value: F


title: Liver, tumor, T3


title: dat_4mo_D186_mut_K4

value: H3K4me3 (Cell Signaling, 9751)

value: 4 months


title: IMSA031_S

value: female

tag: age screened

value: S

tag: batch

tag: condition


title: Hu220OSCSWS1


title: dat_4mo_D186_mut_K27

value: mDA

tag: Sex


title: IMSA028_M

tag: subject id


title: Hu216OSTMS1

source_name: Trabecular meshwork

value: Trabecular meshwork


title: Hu218OSTM


title: 120_Batch2_049_1

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the enrolment (n=14) and crossover visit (n=107) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl))  and transported to the laboratory within 4 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were Rawalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 21 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: dat_4mo_D186_mut_input

tag: tissue

tag: cell type

tag: strain

tag: genotype

value: PRC2 mutant

tag: chip antibody

tag: timepoint

tag: biological replicate

tag: Sex


title: IMSA024_H

value: PBMC

value: male

tag: age screened

tag: disease state

value: H

tag: batch

tag: condition

value: healthy

tag: subject id


title: IMSA034_M

value: M

value: ast


title: Hu216OSTMS2

tag: site

value: Left Eye

tag: donor

tag: 10x kit version


title: 121_Batch2_174_1

tag: sampleid metadata

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: 118_Batch2_096_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv


title: HAP1, Input

city: Helsinki

first: Paivi

last: Pihlajamaa

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq (version 2.20).
The reads were aligned to human genome (hg19) with bowtie2 (version 2.2.4) using default parameters.
Peaks were called using MACS2 (version 2.1.1)  against IgG or input with default narrow peak parameters.
Assembly: hg19
Supplementary files format and content: bedGraph (for all), narrowPeak (except for Input and IgG samples)

growth_protocol: Cells were maintained in low-density cultures in Iscove’s Modified Dulbecco’s Medium (IMDM) with 10% FBS, 2 nM L-glutamine, and 1% antibiotics at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using micro-tip sonicator (Misonix Inc).
Chromatin immunoprecipitation (ChIP) was performed as previously described (PMID: 28473536). Briefly, crosslinked and sonicated chromatin was immunoprecipitated using Dynal-bead coupled antibodies, followed by standard ChIP-seq library preparation with NEBNext Ultra II DNA Library Prep kit (New England Biolabs) for Illumina sequencing.

tag: cell line

tag: cell type

value: near-haploid cell line derived from the chronic myelogenous leukemia cell line KBM-7

tag: chip antibody


title: HAP1, MYC

value: anti-MYC (Millipore #06-340)


title: IMSA027_S

tag: tissue

tag: Sex

value: female

tag: age screened

tag: disease state

value: S

tag: batch

tag: condition

tag: subject id


title: IMSA022_S


title: HAP1, rIgG

value: normal rabbit IgG (SantaCruz sc-2027)


title: 114_Batch2_177_1

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: HNRNPKsi2_2

city: Gothenburg

first: Meena

last: Kanduri

address: Bruna starket 16

department: Department of Laboratory Medicine

institute: Gothenburg University

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample analyzed

source_name: Cancer cell line

extract_protocol:
Cells were collected 48 hours post-transfection for RNA extraction. Total RNA was extracted using Trizol. Cytoplasmic and Nuclear RNA was extracted using RLN1 and RLN2 buffers lysing cytoplamic and Nuclear RNAs sepcifically followed by Trizol extraction.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat # RS-122-2201). mRNA sequencing on 100PE of DNBseq platform

treatment_protocol: HeLa cells were routinely cultured in DMEM media supplemented with 10% FBS. Stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

tag: cell line

value: HeLa

tag: shRNA

value: hnRNPK siRNA2

tag: tissue

value: Cervix, Uterus

tag: molecule

value: total RNA


title: IMSA026_S

value: PBMC

tag: Sex

tag: cell type

tag: age screened

tag: disease state

tag: batch

tag: condition

tag: subject id


title: 115_Batch2_177_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

value: Pos

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc


title: IMSA015_M

tag: tissue

tag: Sex

tag: cell type

tag: age screened

tag: disease state

value: M

tag: batch

tag: condition

value: ast

tag: subject id


title: HAP1, H3K27ac

tag: cell line

value: near-haploid cell line derived from the chronic myelogenous leukemia cell line KBM-7

tag: chip antibody

value: anti-H3K27ac (Abcam #ab4729)


title: 119_Batch2_096_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: HNRNPKsi2_1

tag: cell line

value: HeLa

tag: shRNA

tag: tissue

tag: molecule


title: IMSA023_M

tag: Sex

value: female

tag: cell type

tag: age screened

tag: disease state

tag: batch

tag: condition

tag: subject id


title: 113_Batch2_160_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc


title: IMSA013_S

tag: tissue

tag: Sex

value: male

tag: cell type

tag: age screened

tag: disease state

value: S

tag: batch

tag: condition

tag: subject id


title: HNRNPKsi1_1

tag: cell line

tag: shRNA

value: hnRNPK siRNA1

value: Cervix, Uterus

tag: molecule

value: total RNA


title: HNsi2_NucRNA_2

value: hnRNPK siRNA2

value: Nuclear RNA


title: HNRNPKsi1_2


title: 117_Batch2_077_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: 112_Batch2_160_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: non-HC

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc


title: 116_Batch2_077_1

tag: sampleid metadata

tag: subject id

tag: batch

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: HNsi2_cytoRNA_2

tag: cell line

tag: shRNA

tag: tissue

tag: molecule

value: Cytoplasmic RNA


title: IMSA021_H

value: PBMC

tag: Sex

tag: cell type

tag: age screened

tag: disease state

value: H

tag: batch

tag: condition

value: healthy

tag: subject id


title: 111_Batch2_131_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

tag: hc method

value: NETEN

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc


title: Hela_consi1

tag: cell line

value: HeLa

tag: shRNA

value: control siRNA

tag: tissue

tag: molecule


title: IMSA020_H

tag: Sex

value: female

tag: cell type

tag: age screened

tag: disease state

tag: batch

tag: condition

tag: subject id


title: 110_Batch2_137_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host

tag: cumulative number of reads

tag: median cv coverage


title: IMSA010_M

tag: tissue

tag: Sex

value: male

tag: cell type

tag: age screened

tag: disease state

value: M

tag: batch

tag: condition

value: ast

tag: subject id


title: HNsi1_NucRNA_2

tag: cell line

tag: shRNA

value: hnRNPK siRNA1

value: Cervix, Uterus

tag: molecule

value: Nuclear RNA


title: IMSA007_S

value: PBMC

value: S


title: HNsi2_NucRNA_1

value: hnRNPK siRNA2


title: IMSA006_M


title: Pt14Lens

source_name: Lens

tag: site

value: Lens

value: Right Eye

tag: donor

tag: 10x kit version


title: IMSA012_H

value: H

value: healthy


title: IMSA005_M

value: female


title: Pt14Cornea

source_name: Cornea

value: Cornea

value: Left Eye


title: IMSA004_S


title: 105_Batch2_095_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Hu235OSTM

tag: site

value: Trabecular meshwork

tag: tissue

tag: donor

tag: 10x kit version


title: consi_NucRNA_1

tag: cell line

value: HeLa

tag: shRNA

value: control siRNA

value: Cervix, Uterus

tag: molecule


title: consi_NucRNA_2

value: Nuclear RNA


title: IMSA011_M

value: PBMC

tag: Sex

tag: cell type

tag: age screened

tag: disease state

value: M

tag: batch

tag: condition

value: ast

tag: subject id


title: HNsi2_cytoRNA_1

value: hnRNPK siRNA2

value: Cytoplasmic RNA


title: Hela_consi2

value: total RNA


title: IMSA008_M

value: male


title: P3HR-1 cells, SHIN1 rep2

first: Rui

last: Guo

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
Genome_build: GRCh37.83
Supplementary_files_format_and_content: P3HR-1 processed data.csv (raw counts of genes).

molecule: polyA RNA

growth_protocol: P3HR-1 cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine for 3 days.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: For methionine restriction, P3HR-1 cells were washed with PBS and then cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.01mM L-methionine for 3 days. Control cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine for 3 days. Control or  methionine restricted cells were then subjected to RNAseq analysis. For SHIN1 treatment, P3HR-1 cells were treated with 10uM SHIN1 for 3 days. 1mM sodium formate was used to rescue the SHIN1 effects.

value: Burkitt Lymphoma cells

tag: treatment

value: SHIN1 treated P3HR-1 cells


title: 109_Batch2_025_2

tag: sampleid metadata

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: 100_Batch2_059_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

value: Int

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: number of reads uniquely mapped to host


title: 104_Batch2_089_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: P3HR-1 cells, MR Rep2

tag: cell line

tag: cell type

tag: treatment

value: methionine restricted P3HR-1 cells


title: HNsi1_NucRNA_1

value: HeLa

tag: shRNA

value: hnRNPK siRNA1

tag: tissue

value: Cervix, Uterus

tag: molecule

value: Nuclear RNA


title: HNsi1_cytoRNA_2

value: Cytoplasmic RNA


title: 97_Batch2_127_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: number of reads uniquely mapped to host


title: 107_Batch2_139_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: 106_Batch2_140_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: number of reads uniquely mapped to host


title: Hu220OSTM

tag: site

value: Trabecular meshwork

tag: tissue

value: Left Eye

tag: donor

tag: 10x kit version


title: P3HR-1 cells, SHIN1+Formate rep2

tag: cell line

tag: cell type

value: Burkitt Lymphoma cells

tag: treatment

value: SHIN1+Formate treated P3HR-1 cells


title: 108_Batch2_147_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Hu235OSCSW

tag: site

value: Cornea sclera wedge

tag: tissue

tag: donor

tag: 10x kit version


title: 102_Batch2_074_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: number of reads uniquely mapped to host


title: Hu220OSCB

tag: site

value: Ciliary body

tag: tissue

tag: donor

tag: 10x kit version


title: Hu235CB


title: P3HR-1 cells, SHIN1+Formate rep1

tag: cell line

tag: cell type

tag: treatment


title: 95_Batch2_037_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: consi_cytoRNA_1

tag: cell line

value: HeLa

tag: shRNA

value: control siRNA

tag: tissue

tag: molecule


title: HNsi1_cytoRNA_1

value: hnRNPK siRNA1

value: Cervix, Uterus


title: 101_Batch2_066_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: number of reads uniquely mapped to host


title: 94_Batch2_170_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: any sti no tv

tag: sti prior visit

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Rael cells, sgMAT2A Rep3

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
Genome_build: GRCh37.83
Supplementary_files_format_and_content: Rael_processed_data.csv (raw counts of genes).

source_name: Rael

growth_protocol: For control of the methionine restriction experiment, Rael cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine. For methionine restriction, Rael cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.01mM L-methionine. For CRISPR KO experiments, Rael cells were cultured in RPMI-1640 supplemented with 10% regular FBS.

treatment_protocol: For methionine restriction, Rael cells were washed with PBS and then cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.01mM L-methionine for 3 days. Control cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine for 3 days. Control or  methionine restricted cells were then subjected to RNAseq analysis. For CRISPR KO, Rael cells expressing control, AHCY, or MAT2A sgRNAs were subjected to the RNAseq analysis.

tag: cell line

value: Rael

tag: cell type

tag: treatment

value: Rael cells expressing MAT2A sgRNA


title: P3HR-1 cells, SHIN1 rep1

value: SHIN1 treated P3HR-1 cells


title: Hu220235cIrisS2

source_name: Iris

tag: site

value: Iris

tag: tissue

value: Left Eye

tag: donor

value: Hu0220/Hu0235 pooled

tag: 10x kit version


title: 93_Batch2_057_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Hu235IrisS1

tag: site

tag: tissue

tag: donor

tag: 10x kit version


title: consi_cytoRNA_2

tag: cell line

tag: shRNA

tag: molecule

value: Cytoplasmic RNA


title: grp4_rep3

city: Yokohama

first: Aki

last: Soejima-Kusunoki

state: Kanagawa

address: 1000, Kamoshida-cho, Aoba-ku

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

data_processing:
Real Time Analysis (version 3.4.4; Illumina, Inc., CA, U.S.A.) was used for base calls and quality scores.
bcl2fastq2 (version 2.20; Illumina, Inc., CA, U.S.A.) was used for conversion into FASTQ files.
DRAGEN Bio-IT plat form (version 3.6.3; Illumina, Inc., CA, U.S.A.) was used for alignment and quantification.
R (version 3.6.0) was used for principal component analysis.
DESeq2 (version 1.26.0) was used for differential expression analysis to identified differentially expressed genes (DEGs).
Enrichment analysis of GO and pathways was performed with the DEGs.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw gene counts or tpm values for every gene and every sample

organism: Rattus norvegicus

source_name: Immortalized neural stem cell

growth_protocol: Neural stem cells were splitted to 96 well plates and cultured in FFNBR (F12, 5%FBS, N2, B27, 1mM RA) media for 4 days to differentiate into motor neuron-like cells. Subsequently, after the culcure media was switched to FNR media (F12, N2, 1mM RA), the cells were cultured for 48 hours and then sampled.

extract_protocol:
From frozen pellets of the cultured cells (>10**6), total RNA was extracted with NucleoSpin RNA (Macherey-Nagel GmbH & Co. KG, Düren, Germany).
Using the total RNA as a template (1.0 ng), the double stranded cDNA was synthe-sized by SMART (Switching Mechanism At 5'End of RNA Template) method with SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc., CA, U.S.A.). The double stranded cDNA was amplified in 13 cycles of PCR. The PCR product was purified by the magnetic bead method with AM Pure XP (Beckman Coulter, Inc., CA, U.S.A.). With Nextera XT DNA Library Prep Kit and Nextera XT Index Kit v2 (Illumina, Inc., CA, U.S.A.), the double stranded cDNA was fragmented by tagmentation reaction using transposon and then both ends of the fragmented cDNA was ligated with adapter sequences. The ligated cDNA (0.2 ng) was amplified in 12 cycles of PCR using the primers having a unique sequence for each sample. The PCR products for all samples were pooled into one library.

treatment_protocol: Adenoviruses expressing C-termial fragment of TDP-43 and/or edaravone (50uM) were added at the same time as the media was switched. Ethacrynic acid (20 uM) was added 24 hours after the media was switched.

value: Immortalized neural stem cell

tag: treatment

value: TDP43+Ethacrynic acid+Edaravone


title: grp3_rep3

value: TDP43+Ethacrynic acid


title: Mel_ST rep2

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

institute: CRG

data_processing:
Base-calling was done using Illumina's bcl2fastq program
The GRAPE pipeline for automatised RNAseq analysis was followed (https://github.com/guigolab/grape-nf). The mapping was performed with STAR to Homo Sapiens GRCh38 with STAR 2.4.0j, and the quantification with RSEM 1.2.21.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with abundance quantification for every gene and every sample (RSEM output)

source_name: Cell line

growth_protocol: UACC-257 and SK-MEL-147 cells were grown in DMEM, high glucose, pyruvate, and GlutaMax (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and 1% penicillin-streptomycin (Gibco). Immortalized melanocytes (Mel-ST), were grown in the same conditions except for 7% FBS. All human cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Samples were extracted with Trizol and treated with Turbo DNAse kit (Ambion)
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep kit from Illumina

tag: tumor stage

value: Immortalized melanocytes


title: 92_Batch2_036_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: 98_Batch2_040_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

value: NETEN

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

value: High

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Hu235Cornea

tag: site

value: Cornea

tag: tissue

tag: donor

tag: 10x kit version


title: Hu220235cIrisS1

value: Iris

value: Left Eye


title: Rael cells, sgMAT2A Rep1

tag: cell line

value: Rael

tag: cell type

value: Burkitt Lymphoma cells

tag: treatment

value: Rael cells expressing MAT2A sgRNA


title: grp3_rep2

value: Immortalized neural stem cell


title: Hu235IrisS2


title: Hu218OSmAll

source_name: Macula

value: Macula


title: P3HR-1 cells, MR Rep1

value: methionine restricted P3HR-1 cells


title: grp3_rep1

value: TDP43+Ethacrynic acid


title: 87_Batch2_130_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Hu218Iris

tag: site

tag: tissue

tag: donor

tag: 10x kit version


title: Rael cells, sgAHCY Rep1

tag: cell line

tag: cell type

tag: treatment

value: Rael cells expressing AHCY sgRNA


title: 85_Batch2_144_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: SK_MEL_147 rep2

tag: tumor stage

value: Metastatic melanoma

tag: cell line


title: Hu218Cornea

tag: site

value: Cornea

tag: tissue

tag: donor

tag: 10x kit version


title: Mel_ST rep1

value: Immortalized melanocytes


title: SK_MEL_147 rep1


title: 96_Batch2_041_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

value: NETEN

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: grp1_rep3

tag: tissue

tag: cell line

tag: treatment


title: grp1_rep2


title: P3HR-1 cells, Control Rep2

tag: cell type

value: Burkitt Lymphoma cells

value: Control P3HR-1 cells


title: 84_Batch2_132_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Int

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: P3HR-1 cells, Control Rep1

tag: cell line

tag: cell type

tag: treatment


title: Hu220Iris

tag: site

value: Iris

tag: tissue

value: Left Eye

tag: donor

tag: 10x kit version


title: grp4_rep2

value: Immortalized neural stem cell

value: TDP43+Ethacrynic acid+Edaravone


title: 83_Batch2_051_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

value: CST-III

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: grp1_rep1

tag: tissue

tag: cell line

tag: treatment


title: Rael cells, MR Rep2

value: Rael

tag: cell type

value: methionine restricted Rael cells


title: 80_Batch2_028_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Hu220Cornea

tag: site

value: Cornea

tag: tissue

tag: donor

tag: 10x kit version


title: Rael cells, MR Rep1

tag: cell line

tag: cell type

tag: treatment


title: 81_Batch2_055_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: grp4_rep1

tag: tissue

tag: cell line

tag: treatment


title: Rael cells, sgMAT2A Rep2

tag: cell type

value: Burkitt Lymphoma cells

value: Rael cells expressing MAT2A sgRNA


title: Hu216218cIrisS2

tag: site

value: 0216 right eye/0218 left eye

tag: donor

value: Hu0216/Hu0218 pooled

tag: 10x kit version


title: 78_Batch2_087_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

value: NETEN

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Control - Fatty Adequate Hepatic Function Liver - 3 hours perfusion - replicate 3

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

data_processing:
The sequencing libraries were clustered on 3 lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: hg38
Supplementary files format and content: Raw hit counts table in text file format.

source_name: Liver

extract_protocol:
Tissues samples from livers taken immediately prior to perfusion and after 3 and 6 hours of perfusion were used for bulk transcriptome sequencing. Core needle biopsies from the right liver lobe were collected in RNAlater solution (Sigma-MilleporeMillipore, Waltham, MA, USA) and stored overnight at 4 Celsius. Tissue samples were then removed from solution and stored at -80 Celsius. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer guidelines.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Grafts were perfused for 12 hours on the Liver Assist device (Organ Assist, Groningen, Netherlands) using a previously described protocol (Raigani et al. Clin Transplant. 2020 Nov;34(11):e14069, PMID 32860634). Briefly, perfusate composition consisted of O+ packed red blood cells, human albumin, Lactated Ringer’s solution, and heparin. Bile salts (taurocholate) and lipid-free parenteral nutrition were continuously infused. Perfusate, bile, and tissue biopsies were collected and analyzed at multiple time points. Livers were deemed to be "viable" if they satisfied the following criteria: perfusate lactate < 2.5mmol/L and two or more of the following minor criteria within 4 hours of starting perfusion: a) perfusate pH >7.30, b) arterial flow > 150mL/min and portal flow > 500mL/min, c) evidence of glucose metabolism, d) bile production, and e) visually assessed homogenous perfusion. Livers that failed to meet these criteria were deemed "nonviable".

tag: liver id

tag: lean or fatty

value: Fatty

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

value: Control

tag: treatment

value: perfusion, 3 hours

tag: condition replicate


title: Control - Fatty Adequate Hepatic Function Liver - 0 hours perfusion - replicate 2

value: perfusion, 0 hours


title: Hu216CB

tag: site

value: Ciliary body

tag: tissue

value: Right Eye

tag: donor

tag: 10x kit version


title: 88_Batch2_149_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: 77_Batch2_039_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Rael cells, Control Rep1

tag: cell line

value: Rael

tag: cell type

value: Burkitt Lymphoma cells

tag: treatment

value: Control Rael cells


title: Hu2160SCSW

tag: site

value: Cornea sclera wedge

tag: tissue

value: Left Eye

tag: donor

tag: 10x kit version


title: Rael cells, Control Rep2


title: Control - Fatty Adequate Hepatic Function Liver - 6 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

value: perfusion, 6 hours

tag: condition replicate


title: Rael cells, sgAHCY Rep2

value: Rael cells expressing AHCY sgRNA


title: Hu218OSCSW


title: 76_Batch2_172_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: grp2_rep3

tag: tissue

value: Immortalized neural stem cell

tag: cell line

tag: treatment

value: Edaravone


title: Hu2018Lens

tag: site

value: Lens

tag: donor

tag: 10x kit version


title: 86_Batch2_086_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: grp2_rep2

tag: tissue

tag: cell line

tag: treatment


title: Sample 6

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

data_processing:
After quality control using fastqc and mapping against the human GRCh38 genome build, alignment was done with STAR, reads counted with HTSeq-Count using Gencode v22 as gene model.
Genome_build: GRCh38
Supplementary_files_format_and_content: BAM files and raw counts of gene expression

source_name: Cell Line

growth_protocol: Cell lines were maintained in RPMI culture medium supplemented with 10% FBS and 1% glutamine, at 37°C with 5% CO2. A2780 cells were initially transfected with CRISPR/Cas9 plasmid directed against exon 1 of CDK12 (U6gRNA-Cas9-2A-GFP, Sigma-Aldrich)

extract_protocol:
Total RNA from cell lines was purified with the Maxwell 16 Total RNA Purification Kit (Promega) .
For RNA-Seq we used the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc., Ipswich, MA, USA) and the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) for cDNA synthesis and addition of barcode sequences. The pre-pools sequenced were performed using the NextSeq 500 (Illumina, San Diego, CA, USA) with the NextSeq 500/550 High Output Kit v2.5 (75 cycles; Illumina).
Stranded, single-ended 75bp-long sequencing reads.

tag: genotype

value: CDK12 KO


title: Rael cells, sgAHCY Rep3

tag: cell type


title: grp2_rep1


title: Rael cells, sgCTRL Rep3

value: Rael cells expressing control sgRNA


title: 73_Batch2_159_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: yeast cells

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Rael cells, sgCTRL Rep2

tag: cell line

value: Rael

tag: cell type

value: Burkitt Lymphoma cells

tag: treatment


title: Hu216ODCornea

tag: site

value: Cornea

tag: tissue

value: Right Eye

tag: donor

tag: 10x kit version


title: Rael cells, sgCTRL Rep1


title: 72_Batch2_128_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: number of reads uniquely mapped to host


title: Rael cells, MR Rep3

tag: cell line

tag: cell type

tag: treatment

value: methionine restricted Rael cells


title: Hu056316ODmaculaNeuNPos

tag: site

value: Macula

tag: tissue

tag: donor

tag: 10x kit version


title: Hu216IrisS2

value: Iris

value: Left Eye


title: Sample 2

tag: genotype

value: WT


title: Hu216IrisS1


title: 82_Batch2_079_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

value: CCVR

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Control - Fatty Inadequate Hepatic Function Liver - 0 hours perfusion - replicate 3

tag: liver id

tag: lean or fatty

value: Fatty

tag: transplant viability

value: Inadequate Hepatic Function

tag: agent

value: Control

tag: treatment

value: perfusion, 0 hours

tag: condition replicate


title: Control - Fatty Adequate Hepatic Function Liver - 0 hours perfusion - replicate 3

value: Adequate Hepatic Function


title: Hu216Cornea

tag: site

tag: tissue

tag: donor

tag: 10x kit version


title: Control - Fatty Inadequate Hepatic Function Liver - 3 hours perfusion - replicate 3

value: perfusion, 3 hours


title: 79_Batch2_033_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: COC

tag: hc method

tag: cst

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: number of reads uniquely mapped to host


title: Rael cells, Control Rep3

tag: cell line

value: Rael

tag: cell type

value: Burkitt Lymphoma cells

tag: treatment

value: Control Rael cells


title: bulk_Queen_rep2

city: Kunming

first: Liangliang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

data_processing:
The 10X samples were each processed by the Cell Ranger v3.1.0 count pipelines to generate single-feature barcode matrices.
The feature barcode matrices of each sample were processed by Seurat version 3.1.5.
For bulk RNA-seq libraries, adapters were trimmed off with the Trimmomatic program v0.39. And  the paired reads were aligned to the honeybee reference genome using STAR softwar v2.7.9. STAR mapping produced reads that were accurately quantified by the RSEM program to obtain count matrices for gene expression. The count matrices were processed with the DEseq2 v1.32.0.
Genome_build: assembly Amel_HAv3.1
Supplementary_files_format_and_content: Single-feature barcode matrices
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Apis mellifera

source_name: Brain cells

extract_protocol:
For single cell libraries, cell suspension was collected after the whole brain was dissected. For bulk  libraries,  Five adult brains were pooled and homogenized in Trizol reagent to extract the total RNA.
For single cell libraries, single-cell 3' gene expression libraries were generated following the manufacturer’s instructions (10X Genomics#1000121, Chromium Next GEM Single Cell 3' Reagent Kits v3.1). For bulk  libraries, the sequencing libraries was  were generated following the manufacturer’s instructions  VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme#NR605).

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: queen


title: Control - Fatty Adequate Hepatic Function Liver - 6 hours perfusion - replicate 3

tag: liver id

tag: lean or fatty

tag: transplant viability

tag: agent

value: perfusion, 6 hours

tag: condition replicate


title: Hu216218cIrisS1

tag: site

value: Iris

value: 0216 right eye/0218 left eye

tag: donor

value: Hu0216/Hu0218 pooled

tag: 10x kit version


title: MB231 TLX siTLX 2

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 South Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

data_processing:
Transcript abundance was quantified using Kallisto (v0.44.0) pseudoalignment, using index built from a transcriptome fasta of Homo sapiens build GRCh38 (Ensembl).
Transcript abundance scaled by the average transcript length and to library size was subsequently summarized to gene-level counts using R package Tximport.
After keeping all the genes that were expressed in at least 1 sample, 27548 genes were left for downstream analysis, and differentially expressed gene analysis was performed using R packages Limma-voom and EdgeR on the logCPM values.
False discovery rate (FDR) method was used to correct for multiple testing.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing LogCPM gene values for all samples
Supplementary_files_format_and_content: tab delimited text file containing the fold change, raw p-value, and FDR values for comparisons between different treatment groups

source_name: Triple Negative Breast Cancer Cells

growth_protocol: MDA-MB-231 and MDA-MB-468 cells were grown in DMEM supplemented with 10 % FBS and 1% penicillin-streptomycin antibiotic mixture. MDA-MB-231 control and TLX-overexpressing cells were seeded in 6-well plates at a density of 0.3-0.4 x 106 cells/well for 24 h.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.

treatment_protocol: Cells were transfected for 48 h with either a universal negative control siRNA or with a TLX-targeting siRNA using DharmaFECT 4 Transfection Reagent.

value: Breast Adenocarcinoma

tag: genotype/treatment

value: TLX overexpressing cells treated with an siRNA against TLX (TLX+siTLX)


title: Control - Fatty Inadequate Hepatic Function Liver - 6 hours perfusion - replicate 2

value: Fatty

value: Inadequate Hepatic Function

value: Control


title: 75_Batch2_164_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Control - Fatty Adequate Hepatic Function Liver - 3 hours perfusion - replicate 2

tag: liver id

tag: lean or fatty

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

tag: treatment

value: perfusion, 3 hours

tag: condition replicate


title: MB231 TLX siTLX 1

tag: cell type

tag: cell line

tag: genotype/treatment


title: 67_Batch2_068_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: CCVR

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

value: Int

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: number of reads uniquely mapped to host


title: bulk_Nurse_rep1

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: nurse


title: Hu1635Lens

tag: site

value: Lens

value: Left Eye

tag: donor

tag: 10x kit version


title: Excluded Control - Fatty Adequate Hepatic Function Liver - 0 hours perfusion - replicate 1

tag: liver id

value: Excluded

tag: lean or fatty

value: Fatty

tag: transplant viability

tag: agent

value: Control

tag: treatment

value: perfusion, 0 hours

tag: condition replicate


title: 74_Batch2_155_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

value: NETEN

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: High

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: cumulative number of reads

tag: median cv coverage


title: Sample 4

tag: cell line

tag: genotype

value: CDK12 KO


title: Hu088716OSmaculaNeuNPos

tag: site

value: Macula

tag: tissue

value: Right Eye

tag: donor

tag: 10x kit version


title: Excluded Control - Fatty Adequate Hepatic Function Liver - 6 hours perfusion - replicate 1

tag: liver id

tag: lean or fatty

tag: transplant viability

value: Adequate Hepatic Function

tag: agent

tag: treatment

value: perfusion, 6 hours

tag: condition replicate


title: MB231 TLX siCTL 1

tag: cell type

value: Breast Adenocarcinoma

tag: genotype/treatment

value: TLX overexpressing cells treated with control siRNA (TLX+siCTL)


title: Sample 5


title: Hu082219ODmacula


title: Excluded Control - Fatty Adequate Hepatic Function Liver - 3 hours perfusion - replicate 1

value: perfusion, 3 hours


title: 71_Batch2_114_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-IV

tag: shannon

tag: bv

value: Pos

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: Sample 1

tag: cell line

tag: genotype

value: WT


title: 65_Batch2_099_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

tag: shannon

tag: bv

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

value: Low

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: ng

tag: tv

tag: cumulative number of reads

tag: median cv coverage


title: Control - Fatty Inadequate Hepatic Function Liver - 3 hours perfusion - replicate 1

tag: liver id

tag: lean or fatty

value: Fatty

tag: transplant viability

value: Inadequate Hepatic Function

tag: agent

tag: treatment

tag: condition replicate


title: Hu032616ODmaculaNeuNPos

tag: site

tag: tissue

tag: donor

tag: 10x kit version


title: Sample 3

tag: cell line

tag: genotype


title: 70_Batch2_165_2

tag: sampleid metadata

tag: subject id

tag: batch

tag: visit number

tag: assigned hc

tag: hc method

tag: cst

value: CST-I

tag: shannon

tag: bv

value: Neg

tag: nugent score

tag: bv prior

tag: ph

tag: inflammation category kmeans

tag: sti bacterial any

tag: any sti no tv

tag: sti prior visit

tag: ct

tag: mg

tag: multiple stis

tag: yeast cells

tag: vag ph

tag: antibiotic any

tag: ifny

tag: tnfa

tag: rin

tag: totalyield

tag: cdnaconc

tag: enrichedlibconc

tag: avsize

tag: molarity

tag: number of reads uniquely mapped to host


title: MB231 TLX siTLX 3

tag: cell type

tag: cell line

tag: genotype/treatment

value: TLX overexpressing cells treated with an siRNA against TLX (TLX+siTLX)