title: RGC380

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age


title: 2,4-BPS_0.01_23

status: Public on Aug 18 2022

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

growth_protocol: MCF-7 cells (ATCC, Manassas, VA) were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Wisent Bioproducts), and 1% penicillin and streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq gene expression analysis was conducted on exposed and control MCF-7 cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer?s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer?s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 500/550 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 500 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were maintained for 24 hours in phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) and seeded  into 96-well plates at a density of 2.5 × 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS to eliminate estrogenic components. The next day the medium was removed and replaced with DMEM with 5% CD-FBS containing the chemicals of interest. Cells were exposed in quadruplicate in separate 96-well plates to BPA and 15 alternative chemicals at 10 different concentrations (0.0005, 0.001, 0.01,0.1, 0.5, 1, 5, 10, 50, 100 µM), the positive control 17?-estradiol (E2; 0.0001, 0.001, 0.01, 0.1, 1, 10 nM), dexamethasone (Dex ? a non ER-interacting control; 0.0001, 0.001, 0.01, 0.1, 1 µM) alongside solvent controls (0.1% DMSO; four solvent controls per plate) for 48 hours.

value: breast cancer

tag: cell line

tag: cell type

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

tag: dose

tag: treatment

tag: batch

value: Plate 1A index E

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: GGGTTGTTA

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn

tag: iupac name


title: HaCAT-siControl-replicate_IP

city: Shanghai

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

country: China

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered by Trimmomatic.
Qualified reads were then mapped to hg38 genome using STAR.
Peak calling was performed by MetPeak package as follow:metpeak(GENE_ANNO_GTF = gtf,IP_BAM = ip,INPUT_BAM = input,EXPERIMENT_NAME = name );Cutoff:PEAK_CUTOFF_FDR=0.05, FOLD_ENRICHMENT=1 .
bed files were generated using the bedtools.
Assembly: hg38
Supplementary files format and content: bed

source_name: HaCAT

growth_protocol: HaCAT cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% P/S (Gibco) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA from Epidermis or HaCAT cells was extracted using Trizol reagent (15596018; Thermo Fisher Scientific, Waltham, MA). Due to the presence of m6A in DNA, total RNA was treated with DNase I (04 716 728 001; Roche Diagnostics, Indianapolis, IN) for 20 minutes at 37 ℃ to remove DNA contamination. The RNA was precipitated using magnetic beads (Thermo Fisher Scientific) according to the manufacutor's protocol. The final pellet was resuspended in ultrapure H2O.
The  library was constructed using SMARTer Stranded Total RNA-Seq Kit-version 2 （Pico Input Mammalian，Takara/Clontech，634413).

treatment_protocol: Knockdown of ALKBH5 in HaCAT cells was realized by transfection with siRNAs. Cells grown in six-well plates were transfected with 200 pmol siRNAs using lipofectamine 3000 transfection reagent (Invitrogen, L3000008) according to the manufactuer’s instructions.

tag: cell line

value: HaCAT

value: Keratinocyte cell line

tag: genotype

value: WT

value: Transfection of scramble siRNA

tag: anti-m6a antibody

value: ABE572, Millipore, Germany


title: Pergafast201_0.01_22

tag: tissue

tag: cell type

tag: chemical

tag: chemical long_name

value: Pergafast 201

value: GCAGATGCA


title: 2,4-BPF_0.01_21

value: 2,4-BPF (BPF Analog)

tag: dose

tag: treatment

tag: batch

tag: sequencing pool

value: AGCAAGGTC


title: RGC385

city: Guangzhou

first: Sheng

last: Liu

address: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Retinal ganglion cells, scRNA-seq

library_source: transcriptomic single cell

data_processing:
Previously published pipeline STAR version 2.7.0
Assembly: mm10
Supplementary files format and content: Comma-Separated Values files and matrix files

organism: Mus musculus

source_name: Retina

extract_protocol:
The retina is isolated and flat-mounted under dim red light (created with BioRender.com). A retinal ganglion cell is patched and its responses to blue and green spotlight stimuli are recorded. The cell content is aspirated. RNA is processed using Smart-seq2 protocol to get transcriptomic data.
the cDNA library was sequenced on the NovaSeq 6000 instrument and 150-bp paired-end reads were set up. Each sample was sequenced to approximately 10 million reads

value: Retinal ganglion cells

tag: strain

tag: age

value: 7-9 weeks old


title: HaCAT-siControl-replicate_Input


title: BADGE_0.01_20

value: breast cancer

value: BADGE

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TTCCGAATT


title: BPS-MAE_0.01_24

tag: cell line

value: adenocarcinoma cell line

value: BPS-MAE

value: Plate 1A index E

value: F

tag: i5 index_id

value: AAGTAGGCT

tag: cas-rn

tag: iupac name


title: BPS_0.01_19

tag: tissue

tag: cell type

tag: chemical

value: BPS

tag: chemical long_name

value: Bisphenol S

value: GGGTTGTTA

value: AAACACCTT


title: HaCAT-siALKBH5_IP

value: HaCAT

value: Keratinocyte cell line

tag: genotype

value: ALKBH5 knockdown

tag: treatment

value: Transfection of ALKBH5 knockdown siRNA

tag: anti-m6a antibody

value: ABE572, Millipore, Germany


title: D-8_0.01_18

value: breast cancer

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: ACAACCATC


title: RGC381

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC383

description: Retinal ganglion cells, scRNA-seq


title: RGC382

description: Retinal ganglion cells, scRNA-seq


title: 4,4-BPF_0.01_17

tag: cell line

value: adenocarcinoma cell line

value: 4,4-BPF (Bisphenol F)

value: Plate 1A index E

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: GTGCATTAG


title: Nor_9

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used Bowtie 1.0.1 to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives. We select mirbase v22 to quantify mature micrornas employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads were considered.
Mapped reads were quantified to GENCODE-v26 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: read count table

extract_protocol:
Total RNA from extracellular vesicles from endometrial fluid was extracted using either the mirVana PARIS kit (Ambion) or the Plasma/Serum RNA Purification kit (Norgen), as detailed in the SAMPLES section
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

treatment_protocol: Endometrial fluid was aspirated with a catheter used for embryo transfer (Frydman, Instrumentos Médicos Estériles SA, Spain) connected to a 10 mL syringe, under abdominal ultrasound guidance. Sample extraction was performed by gentle manual application of negative pressure with the syringe. To prevent contamination with cervical mucus, aspiration was interrupted at the internal cervical os. Aspirate volumes ranged from 5 uL up to 50 uL. After the aspiration, the 10 mL syringe was replaced with a 2 mL syringe containing 1.5 mL saline solution and the aspirates were mixed and expelled in a cryogenic tube (5-50 uL of EF + 1500 uL 1XDPBS (Gibco, Thermo Fisher Scientific #14190250). The mixed samples were centrifuged to remove contaminants at 2,000 x g for 5 min and the supernatants were then frozen at −80 °C until processed. The dilution of the supernatants was 1:30 and they had a volume comprised between 400uL and 1300uL. Extracellular vesicle enrichment was done with Total Exosome Isolation Reagent from cell culture media (Invitrogen by ThermoFisher Scientific, #4478359). The EF supernatants were centrifuged at 3000 g for 30 min at 4 ºC, then 400uL were transferred to a fresh tube and 1 volume of the Total Exosome Isolation Reagent (1:1) was added. The mixture was incubated for 30 min at room temperature and then centrifuged at 10,000 g for 1 hour at 4 ºC. The supernatant was discarded and the EVs that were in the pellet were resuspended in 100 uL of 1 x DPBS.

tag: sample type

value: Endometrial fluid

tag: tissue

value: Implantative endometrium


title: HCT116_sonicated_5ng

type: genomic

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 1441 Biggy street

department: Urology

country: USA

institute: USC Keck school of medicine

hyb_protocol: Standard Illumina Procotol

scan_protocol: Illumina iScan technology using standard scanner setting

data_processing: R package 'minfi' was used for data processing and background normalization

label: Cy5 and Cy3

molecule: genomic DNA

source_name: sonicated genomic DNA from HCT117

label_protocol: Standard Illumina Procotol

growth_protocol: McCoy′s 5A Medium w/ 10% FBS and 1% Penicillin-Streptomycin, 37 ℃, 5% CO2

extract_protocol: phenol/chloroform

tag: tag

value: Cell culture


title: HaCAT-siControl_Input

value: HaCAT

tag: cell type

tag: genotype

value: WT

tag: treatment

value: Transfection of scramble siRNA


title: 2,4-BPS_0.001_15

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

value: F

value: AAGACTCTT

tag: i5 index_id

value: TAACGCGTC

tag: cas-rn

tag: iupac name


title: RGC384

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: HaCAT-siALKBH5_Input

tag: cell line

value: Keratinocyte cell line

value: ALKBH5 knockdown

value: Transfection of ALKBH5 knockdown siRNA

tag: anti-m6a antibody


title: BPS-MAE_0.001_16

value: breast cancer

value: BPS-MAE

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: AAGTAGGCT


title: Pergafast201_0.001_14

tag: tissue

tag: cell type

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

value: Pergafast 201

tag: treatment

value: Plate 1A index E

value: GCAGATGCA


title: HaCAT-replicate_2_IP

tag: genotype

value: no  treatment

value: ABE572, Millipore, Germany


title: Nor_6

description: Plasma/Serum RNA Purification kit (Norgen)

source_name: extracellular vesicles from endometrial fluid

tag: sample type

value: Endometrial fluid

value: Implantative endometrium


title: HCT116_sonicated_10ng

source_name: sonicated genomic DNA from HCT118

tag: tag

value: Cell culture


title: Nor_8


title: RGC386

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: Nor_5


title: RGC387

description: Retinal ganglion cells, scRNA-seq


title: HCT116_200ng

source_name: genomic DNA from HCT120

tag: cell line


title: HCT116_sonicated_1ng

source_name: sonicated genomic DNA from HCT116


title: Nor_7


title: HCT116_sonicated_20ng

source_name: sonicated genomic DNA from HCT119


title: HaCAT-siControl_IP

value: HaCAT

value: Keratinocyte cell line

value: WT

value: Transfection of scramble siRNA

tag: anti-m6a antibody


title: 2,4-BPF_0.001_13

value: breast cancer

value: 2,4-BPF (BPF Analog)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

value: AAGACTCTT

tag: i5 index_id

value: AGCAAGGTC

tag: cas-rn

tag: iupac name


title: HaCAT-replicate_2_Input

tag: cell type

value: no  treatment


title: RGC388

description: Retinal ganglion cells, scRNA-seq

tag: tissue


title: HaCAT-replicate_1_IP

tag: genotype

tag: treatment

value: ABE572, Millipore, Germany


title: RGC389

description: Retinal ganglion cells, scRNA-seq


title: BADGE_0.001_12

value: adenocarcinoma cell line

tag: chemical

value: BADGE

tag: chemical long_name

value: Plate 1A index E

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TTCCGAATT


title: Nor_4

tag: sample type

value: Endometrial fluid

value: Implantative endometrium


title: Nor_3


title: HaCAT-replicate_1_Input

tag: cell line

value: HaCAT

tag: anti-m6a antibody


title: BPS_0.001_11

value: BPS

value: Bisphenol S

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

value: AAACACCTT


title: Human epidermis_2_IP

source_name: Epidermis

tag: tissue

value: Epidermis

tag: cell type

value: primary cell

value: WT


title: Nor_2


title: Human epidermis_2_Input

tag: genotype

tag: treatment


title: 4,4-BPF_0.001_9

value: breast cancer

tag: chemical

tag: chemical long_name

value: 4,4-BPF (Bisphenol F)

value: F

value: AAGACTCTT

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn

tag: iupac name


title: BPS_0.1_27

value: adenocarcinoma cell line

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: GAACTGTAT


title: BPS-MAE_0.0005_8

tag: cell line

value: BPS-MAE

tag: dose

tag: batch

value: Plate 1A index E

value: TCCTCAGCC

value: AAGTAGGCT


title: RGC391

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: RGC393

description: Retinal ganglion cells, scRNA-seq

tag: cell type

tag: tissue


title: RGC392

description: Retinal ganglion cells, scRNA-seq


title: 2,4-BPS_0.0005_7

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

value: TAACGCGTC


title: Nor_30

tag: sample type

value: Endometrial fluid

value: Implantative endometrium


title: RGC394

description: Retinal ganglion cells, scRNA-seq


title: Pergafast201_0.0005_6

value: breast cancer

tag: chemical

tag: chemical long_name

value: Pergafast 201

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn

tag: iupac name


title: Human epidermis_1_IP

value: Epidermis

value: primary cell

tag: genotype

value: WT

value: no  treatment

tag: anti-m6a antibody

value: ABE572, Millipore, Germany


title: RGC395

description: Retinal ganglion cells, scRNA-seq


title: Human epidermis_1_Input


title: 2,4-BPF_0.0005_5

tag: cell line

value: adenocarcinoma cell line

value: 2,4-BPF (BPF Analog)

tag: dose

tag: batch

value: Plate 1A index E

value: F

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: AGCAAGGTC


title: RGC390

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: D-8_0.001_10

tag: chemical

tag: chemical long_name

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

value: AAGACTCTT

value: ACAACCATC


title: SEP_4

city: Xi'an

first: Zhengliang

last: Zhang

address: No. 157, Xiwu Road, Xincheng District

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Reads were aligned to the reference genome (GRCh37/hg19) and Deseq 2 package was used to quantitate FPKMs and differential expression.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text files include content for each Sample

source_name: blood

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The RNA quality and quantity were analyzed by using an Agilent bioanalyzer. RNA-seq libraries were prepared and the sequencing was performed at Katimesbio (Hangzhou, China).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: subject status

value: patients with acute sepsis

value: blood

tag: genotype

tag: time

value: Day 0


title: SEP_3


title: BADGE_0.0005_4

value: breast cancer

tag: cell line

value: BADGE

tag: dose

tag: batch

tag: solvent control

value: TCCTCAGCC

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn

tag: iupac name


title: Nor_23

tag: sample type

value: Endometrial fluid

tag: tissue

value: Non-implantative endometrium


title: D-8_0.0005_2

tag: cell type

value: adenocarcinoma cell line

tag: chemical

tag: chemical long_name

value: Plate 1A index E

tag: well

tag: i7 index_id

tag: index


title: RGC397

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: RGC398

description: Retinal ganglion cells, scRNA-seq


title: Nor_22


title: SEP_5

tag: subject status

tag: genotype

value: WT

tag: treatment

tag: time


title: RGC399

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: Nor_21


title: Nor_26


title: Nor_29


title: Nor_27


title: Nor_28


title: 4,4-BPF_0.0005_1

tag: cell line

value: 4,4-BPF (Bisphenol F)

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: i5 index_id

value: GTGCATTAG


title: iDopa/iAstro 2B cLTP, rep2

city: La Jolla

first: Anne

middle: G

last: Bang

address: 10901 North Torrey Pines Road

department: Prebys Center

institute: Sanford Burnham Prebys Medical Discovery Insititute

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Read counts were compared using the R Bioconductor package DESeq2 based on negative binomial distribution (Love et al., 2014)
Genes were selected as significantly differentially expressed genes with Benjamini-Hochberg–corrected p value< 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized expression (TPM) for every gene and every sample

molecule: polyA RNA

source_name: iDopa Midbrain dopaminergic neuronal population and iAstro astrocytes from FujiFilm Cellular Dynamics, Inc.

extract_protocol:
Triplicate samples were prepared for cLTP and control groups, with each sample comprised of 8 wells combined. Total RNA was isolated using an RNeasy mini kit (Qiagen, 74104) and treated with DNase (Qiagen 79254). Invitrogen Qubit and Agilent TapeStation were used to determine RNA concentration and RNA integrity numbers respectively prior to library preparation.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).
Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

tag: cell type

value: hiPSC-derived midbrain dopaminergic mixed neuronal population (mixture of dopaminergic, glutamatergic, and GABAergic neurons) and astrocytes in co-culture

value: forskolin (50 uM) and rolipram (0.1 uM)

value: cLTP

tag: weeks in cutlure before treatment

tag: timepoint

value: 5 hours post forskolin and rolipram washout


title: iDopa/iAstro 2C cLTP, rep3


title: RGC400

description: Retinal ganglion cells, scRNA-seq

tag: tissue

value: Retina

tag: strain

value: 7-9 weeks old


title: Nor_25

tag: sample type


title: CON_4

tag: subject status

value: health donors

value: blood

tag: genotype

value: Day 0


title: Nor_24

value: Endometrial fluid

value: Non-implantative endometrium


title: SEP_1

value: patients with acute sepsis

tag: treatment

tag: time


title: RGC401

description: Retinal ganglion cells, scRNA-seq

tag: age


title: CON_3

value: WT


title: Nor_20


title: RGC402

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: iDopa/iAstro 2A cLTP, rep1


title: Nor_19


title: iDopa/iAstro 2C control, rep 3

value: 0.2percent Dimethyl sulfoxide (DMSO) vehicle

value: cLTP vehicle control, and also used to assess expression of specific marker genes

value: 5 hours post DMSO washout


title: CON_1


title: RGC408

description: Retinal ganglion cells, scRNA-seq


title: Nor_18


title: Nor_1

value: Implantative endometrium


title: RGC409

description: Retinal ganglion cells, scRNA-seq


title: Nor_17


title: iDopa/iAstro 2B control, rep2

value: hiPSC-derived midbrain dopaminergic mixed neuronal population (mixture of dopaminergic, glutamatergic, and GABAergic neurons) and astrocytes in co-culture


title: CON_2


title: Nor_15


title: Nor_16


title: RGC407

description: Retinal ganglion cells, scRNA-seq


title: RGC396

description: Retinal ganglion cells, scRNA-seq


title: iDopa/iAstro 2A control, rep1


title: iDopa/iAstro 1C control, rep3

value: used to assess expression of specific marker genes


title: RGC404

description: Retinal ganglion cells, scRNA-seq


title: Nor_14


title: RGC403

description: Retinal ganglion cells, scRNA-seq


title: HD 5, PBMC, nTreg, scATAC-seq

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

library_source: genomic single cell

data_processing:
Fastq files were processed with cellranger-atac count pipeline, version 1.2.0.
Assembly: hg38
Supplementary files format and content: hdf5 file,  _fragments.tsv.gz file and_singlecell.csv  from cellranger-atac output

source_name: PBMC

extract_protocol:
Peripheral blood and tumor tissues for scATAC-seq were obtained from healthy individuals and NSCLC patients who underwent a surgery for curative resection at the National Cancer Center Hospital East. Each Treg cell subset [Naive Treg cells (CD45RA+CD25lowFoxP3low CD4+) and eTreg cells (CD45RA–CD25highFoxP3highCD4+)] was sorted with a BD FACSAria Fusion Cell Sorter (BD Biosciences, San Jose, CA) for subsequent scATAC- seq analyses. Naive Treg cells and eTreg cells from healthy individuals’ PBMCs, normal lung tissues, and cancer patients’ TILs were purified for scRNA-seq analyses using Ficoll-Paque or Tumor Tissue Dissociation Reagent (BD Biosciences), which enzymatically dissociate tissues as previously described (PMID: 35852944  ).  Normal lung tissues were resected from the same lung lobe as the lung tumor, but from the area farthest from the tumor (at least >5 cm from the tumor). Because of the limited number of Treg cells in the normal lung tissues, both Treg cells (CD45RA-CD25highCD4+ T cells) and CD8+ T cells (CD45RA-CCR7-CD8+) in normal lung tissues were sorted, and then CD8+ T cells were bioinformatically removed from the downstream analyses of scATAC-seq. Anti-CD3 (clone: UCTH1), anti-CD4 (clone: RPA-T4) and anti-CD45RA (clone: HI100) mAbs were purchased from BD Biosciences. Anti-CCR7 (clone: G043H7) and anti-CD25 (clone: BC96) mAbs were obtained from BioLegend (San Diego, CA). Fixable Viability Dye eFluor 780 was purchased from Thermo Fisher Scientific (Waltham, MA).
scATAC-seq libraries were constructed with Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics) or Chromium Single Cell ATAC Reagent Kits v1 (10x Genomics). The cell lysates of each sample were processed in the Chromium Controller (10x Genomics) to generate single-cell GEMs for sample and cell barcoding.

value: PBMC

value: nTreg cells


title: HD 6, PBMC, eTreg, scATAC-seq

value: eTreg cells


title: HD 4, PBMC, nTreg, scATAC-seq


title: iDopa/iAstro 1A control, rep1


title: HD 6, PBMC, CD4+ CD25+ T, scATAC-seq

value: CD4 positive CD25 postive T cells


title: RGC405

description: Retinal ganglion cells, scRNA-seq

value: Retina

value: 7-9 weeks old


title: Nor_13

value: Endometrial fluid


title: HD 4, PBMC, CD4+ CD25+ T, scATAC-seq


title: RCC-PR3-PTumor3

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.2.0). Human genome hg19 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts. Quality control metrics were used to select cells with total UMI more than 700.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv

source_name: kidney

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Single cells from the tumor and the normal adjacent kidney samples subjected to RBC lysis were surface stained with anti-CD235-PE (Biolegend) for 30 min at 4°C. Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument. All flow cytometry data were analyzed using FlowJo software (Treestar, San Carlos, CA).

tag: condition

value: Tumor

tag: Stage

value: ccRCC

value: No

tag: metastasic sites


title: RGC406

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: HD 4, PBMC, eTreg, scATAC-seq


title: RGC415

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR3-PTumor2


title: RCC-PR3-PTumor1


title: NSCLC 14, normal lung, Treg and CD8+ T, scATAC-seq

source_name: normal lung

value: normal lung

value: Treg cells and CD8 positive T cells


title: Nor_10


title: NSCLC 8, TIL, eTreg, scATAC-seq

source_name: TIL

value: TIL


title: RGC416

description: Retinal ganglion cells, scRNA-seq


title: RGC411

description: Retinal ganglion cells, scRNA-seq


title: Mir_9

description: mirVana PARIS kit (Ambion)

value: Implantative endometrium


title: RCC-PR3-Normal

value: Normal


title: RGC412

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR4-PTumor


title: Mir_8

description: mirVana PARIS kit (Ambion)


title: RCC-PR4-Normal


title: HD 5, PBMC, eTreg, scRNA-seq

data_processing:
Fastq files were processed with cellranger count pipeline, version 6.1.1.
Assembly: hg38
Supplementary files format and content: hdf5 file from cellranger output

extract_protocol:
Peripheral blood and tumor tissues for scRNA-seq were obtained from healthy individuals and NSCLC patients who underwent a surgery for curative resection at the National Cancer Center Hospital East. Each Treg cell subset [Naive Treg cells (CD45RA+CD25lowFoxP3low CD4+) and eTreg cells (CD45RA–CD25highFoxP3highCD4+)] was sorted with a BD FACSAria Fusion Cell Sorter (BD Biosciences, San Jose, CA) for subsequent scRNA- seq analyses. Naive Treg cells and eTreg cells from healthy individuals’ PBMCs, normal lung tissues, and cancer patients’ TILs were purified for scRNA-seq analyses using Ficoll-Paque or Tumor Tissue Dissociation Reagent (BD Biosciences), which enzymatically dissociate tissues as previously described (PMID: 35852944  ).  Normal lung tissues were resected from the same lung lobe as the lung tumor, but from the area farthest from the tumor (at least >5 cm from the tumor). Because of the limited number of Treg cells in the normal lung tissues, both Treg cells (CD45RA-CD25highCD4+ T cells) and CD8+ T cells (CD45RA-CCR7-CD8+) in normal lung tissues were sorted, and then CD8+ T cells were bioinformatically removed from the downstream analyses of scRNA-seq and scATAC-seq. Anti-CD3 (clone: UCTH1), anti-CD4 (clone: RPA-T4) and anti-CD45RA (clone: HI100) mAbs were purchased from BD Biosciences. Anti-CCR7 (clone: G043H7) and anti-CD25 (clone: BC96) mAbs were obtained from BioLegend (San Diego, CA). Fixable Viability Dye eFluor 780 was purchased from Thermo Fisher Scientific (Waltham, MA).
scRNA-seq libraries were constructed with Chromium Next GEM Single Cell 3′Reagent Kits v3.1 (10x Genomics, Pleasanton, CA) according to the manufacturer's instruction. Cell suspensions of each sample were processed in the Chromium Controller (10x Genomics) to generate single-cell gel bead-in-emulsions (GEMs) for sample and cell barcoding.


title: HD 5, PBMC, nTreg, scRNA-seq


title: HD 4, PBMC, eTreg, scRNA-seq


title: NSCLC 13, normal lung, Treg and CD8+ T, scRNA-seq


title: Mir_6

description: mirVana PARIS kit (Ambion)


title: RGC417

description: Retinal ganglion cells, scRNA-seq


title: RGC413

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR1-PTumor

value: pRCC


title: Nor_12


title: RGC418

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR2-PTumor


title: BPS_0.0005_3

value: breast cancer

tag: cell line

value: adenocarcinoma cell line

tag: chemical

value: BPS

tag: chemical long_name

value: Bisphenol S

tag: dose

tag: batch

value: Plate 1A index E

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: well

tag: i7 index_id

tag: index

value: TCCTCAGCC

value: AAACACCTT

tag: cas-rn

tag: iupac name


title: NSCLC 12, normal lung, Treg and CD8+ T, scRNA-seq

tag: tissue

tag: cell type


title: Mir_3

description: mirVana PARIS kit (Ambion)

tag: sample type

value: Endometrial fluid


title: Mir_4

description: mirVana PARIS kit (Ambion)


title: NSCLC 11, normal lung, Treg and CD8+ T, scRNA-seq


title: RGC420

description: Retinal ganglion cells, scRNA-seq

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: NSCLC 8, TIL, eTreg, scRNA-seq

source_name: tumor

value: tumor

value: eTreg cells


title: NSCLC 10, TIL, eTreg, scRNA-seq


title: RGC419

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: RCC-BM2-PTumor2

tag: condition

value: Tumor

tag: Stage

value: ccRCC

tag: treatment

value: No

tag: metastasic sites

value: Bone, lung, adrenal gland, kidney


title: RGC424

description: Retinal ganglion cells, scRNA-seq


title: NSCLC 9, TIL, eTreg, scRNA-seq


title: RGC414

description: Retinal ganglion cells, scRNA-seq


title: Mir_30

description: mirVana PARIS kit (Ambion)

value: Implantative endometrium


title: Mir_2

description: mirVana PARIS kit (Ambion)


title: K562.untreated.RNA.B2

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

description: total RNA with rRNA depletion

data_processing:
The SSB site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the exception that additional filter was used: a read-pair was used only if the first base of the read 2 aligned to the genome.
Assembly: hg19(GRCh37) for human
Supplementary files format and content: BED files contain coordinates of the bases immediately upstream of single-strand breaks in the non-repeat portions of the genome. The 4th columns show the number of reads representing the SSB sites.

extract_protocol:
Cells were either crosslinked with formaldehyde in vivo and fragmented with MNase for the standard SSiNGLe-ILM protocol, or directly used for genomic DNA extraction followed by the SSiNGLe on HMW DNA protocol. For SSiNGLe on HMW DNA, the DNA was extracted directly from K562 cells using the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer’s protocol. One hundred nanograms of the DNA was used directly as input into the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) at the polyA-tailing step with only one modification at the Illumina library construction stage. The step 19 in the procedure corresponding to the 2nd round PCR was performed with all (instead of just the 4 µl used in the standard protocol) DNA from the 1st round PCR. The latter was purified with the 2x volume of the VAHTS DNA Clean Beads (Vazyme) before adding to the 2nd round PCR. Total RNA was extracted using TRNzol Universal (Tiangen, DP424) and Total RNA kit I (Omega, R6834-02) according to the manufacturer’s protocols and quantified using Qubit 3.0 Fluorometer (Life technologies).
The libraries of SSBs were prepared as described here: https://protocolexchange.researchsquare.com/article/pex-920/v2. And the RNA-seq libraries were contructed based on rRNA depletion strategy by Novogene Corporation (Beijing).

tag: cell line

value: chronic myelogenous leukemia cell line

value: untreated


title: Mir_29

description: mirVana PARIS kit (Ambion)

value: Non-implantative endometrium


title: Mir_5

description: mirVana PARIS kit (Ambion)


title: RGC421

description: Retinal ganglion cells, scRNA-seq


title: RGC422

description: Retinal ganglion cells, scRNA-seq


title: RCC-BM2-PTumor1


title: RCC-BM1-Normal

value: Normal


title: RCC-PR5-PTumor3


title: Mir_27

description: mirVana PARIS kit (Ambion)


title: Mir_28

description: mirVana PARIS kit (Ambion)


title: RGC425

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR5-PTumor2


title: RCC-BM1-PTumor

value: Bone


title: RGC423

description: Retinal ganglion cells, scRNA-seq


title: K562.untreated.RNA.B1

description: total RNA with rRNA depletion


title: RCC-PR5-PTumor1


title: K562.SSiNGLe-original.B1

description:
crosslinked MNase-treated nuclei
Classical SSiNGLe protocol

library_source: genomic

value: DMSO


title: Mir_26

description: mirVana PARIS kit (Ambion)

value: Endometrial fluid


title: K562.SSiNGLe-original.B2


title: RGC432

description: Retinal ganglion cells, scRNA-seq

value: Retina


title: K562.SSiNGLe-HMW_DNA.B2

description:
without fragmentation or crosslinked nuclei
SSiNGLe without fragmentation or crosslinking


title: Mir_25

description: mirVana PARIS kit (Ambion)


title: RCC-PR5-Normal


title: K562.untreated.B6

description: crosslinked MNase-treated nuclei


title: RGC435

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: Mir_24

description: mirVana PARIS kit (Ambion)


title: Mir_23

description: mirVana PARIS kit (Ambion)


title: K562.untreated.B5

description: crosslinked MNase-treated nuclei


title: RGC426

description: Retinal ganglion cells, scRNA-seq


title: RCC-PR9-PTumor2

value: Primary RCC tumor Thrombus


title: RCC-PR9-Normal


title: Mir_21

description: mirVana PARIS kit (Ambion)


title: RGC428

description: Retinal ganglion cells, scRNA-seq


title: HEK293_KLF4_K409Q_IP_6

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

description: HEK293_KLF4_K409Q_IP_6 (biol rep 6)

data_processing:
ChIP-seq reads were examined for technical artifacts with FastQC. No aberrant technical behavior was identified.
Reads were trimmed for adapter sequences and decontaminated for sequencing artifacts by BBDuk. Trimming options were set to ktrim=right trimming, mink=11, hdist=1, qin=33, and tpe and tbo options enabled. BBDuk’s list of Illumina sequencing adapters was used to perform adapter trimming. Decontamination was done against PhiX adapters and BBDuk’s database of sequencing artifacts.
Decontaminated reads were aligned to version GRCh38 of the human reference genome using BWA-mem with default options.
Aligned reads were filtered to ensure a minimum of one mapped read per pair, a minimum Phred quality score of 10, and exclusion from the ENCODE genomic region blacklist.
Peaks were called with respect to the input chromatin library using MACS2 with the following options: -g hs -q 0.05 -f BAMPE –keep-dup all.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

growth_protocol: Cells were cultured in EMEM, 10% fetal bovine serum, 2mM glutamine, 1% non-essential amino acids, without antibiotics, at 37oC and 5% CO2.

extract_protocol:
Chromatin was prepared using the truChIP® Chromatin Shearing Kit (PN520154, Covaris) according to the kit procedure. Briefly, 24 hours post-transfection, cells were fixed with formaldehyde and lysed to prepare nuclei. Their chromatin was sheared for 16 minutes/sample in a 1-mL volume using an E220 Evolution sonicator (Covaris) with the instrument settings described in the kit. Five hundred µg of chromatin for each sample was IP-ed with 40 microliters of anti-FLAG® M2 Magnetic Beads (M8823, Sigma-Aldrich) in a rotary holder overnight at 4 oC. The beads were washed once with 1x RIPA Lysis Buffer (20-188, Sigma-Aldrich), followed by four more washes with RIPA Wash buffer (RIPA Lysis buffer with an increased concentration of NaCl to 500 mM). The washed beads were reverse-crosslinked by treating with Proteinase K overnight at 65 oC in a 200-µL volume. Precipitated genomic DNA was purified using a GeneJET PCR Purification Kit (FERK0701, Fisher Scientific).
ChIP-seq libraries were prepared according to Swift Bioscience protocols and were sequenced using 150 bp paired-end sequencing on an Illumina NovaSeq, producing an average of 177,095,140 reads per library.

treatment_protocol: Transient transfections (1 µg of plasmid DNA per 10^6 cells) were carried out using Invitrogen™ Lipofectamine™ LTX Reagent with PLUS™ Reagent (Fisher Scientific, 15-338-100) according to the manufacturer’s instructions.

value: Human embryonic kidney

tag: klf4 genotype

value: KLF4 K409Q

tag: chip antibody

value: anti-FLAG M2 (Sigma-Aldrich, #M8823)


title: RCC-PR7-PTumor

value: Tumor

value: ccRCC


title: RCC-PR8-Normal

value: No


title: RGC429

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells


title: HEK293_KLF4_K409Q_IP_4

description: HEK293_KLF4_K409Q_IP_4 (biol rep 4)


title: RGC430

description: Retinal ganglion cells, scRNA-seq


title: Mir_1

description: mirVana PARIS kit (Ambion)

value: Implantative endometrium


title: HEK293_KLF4_K409Q_IP_5

description: HEK293_KLF4_K409Q_IP_5 (biol rep 5)


title: K562.untreated.B4

description: crosslinked MNase-treated nuclei

value: chronic myelogenous leukemia cell line

value: untreated


title: RCC-PR9-PTumor

value: chemotherapy for collicular lymphoma


title: RCC-PR6-PTumor


title: Mir_19

description: mirVana PARIS kit (Ambion)

value: Non-implantative endometrium


title: RGC427

description: Retinal ganglion cells, scRNA-seq


title: HEK293_KLF4_K409Q_IP_3

description: HEK293_KLF4_K409Q_IP_3 (biol rep 3)


title: Mir_20

description: mirVana PARIS kit (Ambion)


title: Mir_18

description: mirVana PARIS kit (Ambion)


title: RGC433

description: Retinal ganglion cells, scRNA-seq


title: HEK293_KLF4_K409Q_IP_2

description: HEK293_KLF4_K409Q_IP_2 (biol rep 2)


title: RCC-PR6-Normal

value: Normal


title: RGC431

description: Retinal ganglion cells, scRNA-seq


title: HEK293_KLF4_K409Q_IP_1

description: HEK293_KLF4_K409Q_IP_1 (biol rep 1)


title: Mir_17

description: mirVana PARIS kit (Ambion)

value: Endometrial fluid


title: Human7_input_ChIPseq_ZIKVpositive_24h

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq and csRNA-seq reads aligned to the GRCh38/hg38 assembly using STAR were used to generate gene expression FPKM values using HOMER. Gene expression (RNA-seq) was measured using HOMER with the following parameters: analyzeRepeats.pl rna hg38 -count exons -raw -pc 3 -strand - -condenseGenes followed by DESeq normalized regularized logarithm (rlog) normalization values while accounting for individual donors in the design matrix. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific (RNA-seq = exonic reads) reads for each transcript. csRNA-seq reads aligned to the GRCh38/hg38 assembly from three replicates per condition (mock, ZIKV-, ZIKV+) were combined and TSRs identified using HOMER findcsRNATSS.pl with the corresponding combined input and RNA-seq tag directories.
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called using tags from three replicates per condition with input DNA as background using HOMER’s getDifferentialPeaksReplicates.pl using the “-style factor” (5-fold enrichment over background and FDR < 0.001).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: RNA-seq tab-delimited text files include FPKM values for each sample. Tab-delimited BED files containing peak positions for each ChIP-seq experiment or combined replicates for csRNA-seq experiments.

source_name: Human blood monocytes derived

growth_protocol: Human peripheral blood was separated using Histopaque 1077 and centrifuged at 300xg for 30 min at 4˚C. The buffy coat was washed once, and red blood cells were lysed with molecular grade water. Monocytes were negatively selected from the buffy coat using the human pan monocyte isolation kit (Miltenyi Biotec) as described by the manufacturer. Cells were seeded at 1.5 x 10^6 cells/mL onto polystyrene plates and differentiated for 7 days in hDC media composed of RPMI 1640 Medium, GlutaMAX™ Supplement, 1% penicillin/streptomycin, 2.5% HEPES buffer, and freshly added cytokines including 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) and 100 ng/ml recombinant human interleukin 4 (rhIL-4). Cells were incubated at 37˚C, 5% CO2 and media was changed every 2-3 days.

extract_protocol:
For RNA-seq and csRNA-seq, after ZIKV infection of hDCs for 24 hours, cells were collected and stained with Zombie Violet™ Fixable Viability stain (BioLegend) for 20 min at 4˚C. After washing, cells were fixed and permeabilized with 4% paraformadehyde (PFA), 0.1% saponin in the presence of RNasin Ribonuclease inhibitor (400 U/mL). After centrifugation, samples were resuspended in wash buffer (0.2% BSA, 0.1% saponin and 400 U/mL of RNasin Ribonuclease inhibitor). Sample were blocked with human Fc blocker diluted in staining buffer (1% Bovine serum albumin (BSA), 0.1% saponin, 1600 U/mL RNasin Ribonuclease inhibitor) for 5 min, 4˚C. Then, 4G2-AF647 antibody was added to samples and incubated for 30 min, 4˚C. Samples were centrifuged at 1000xg for 3 min, 4˚C. Cells were washed using wash buffer and centrifuged at 1000xg for 3 min, 4˚C. Samples were resuspended in sort buffer containing 0.5% BSA and 1600 U/mL of RNase inhibitor in 1XPBS and sorted into ZIKV+ or DENV+ and ZIKV− or DENV- cells on a FACSAria cell sorter (BD Biosciences). After sorting, cells were pelleted at 4oC, supernatant discarded and total RNA isolated using Ambion’s RecoverAll Total Nucleic Acid Isolation Kit [AM1975], starting at the protease digestion step. All steps were performed per manufacturer recommendations with the following modification. Cells were incubated in digestion buffer for 3 hours at 50oC supplemented with RNasin Plus RNase Inhibitor. RNA was treated with in column DNase per manufacturer instructions, eluted and RNA quality determined by BioAnalyzer using the Eukaryote Total RNA Pico Chip. Samples with RIN values greater than 8.0 were used for library preparation. For chromatin immunoprecipitation-sequencing (ChIP-seq) experiments, moDCs were cross-linked with 4 mM disuccinimidyl glutarate (DSG) in PBS for 30 minutes at RT followed by 1% formaldehyde for 15 minutes at RT and quenched with 0.125 M glycine. Preparation of moDCs for FACS was performed as described above for RNA-seq except that 1x cOmplete protease inhibitors (Roche) were included in all buffers instead of RNasin Plus RNase Inhibitor. After separation by FACS, cells were washed, separated into 500,000 cell aliquots, pelleted, snap-frozen and stored at -80°C.
For RNA-seq, RNA libraries were generated using the TruSeq stranded total RNA-seq [Illumina] kit per manufacturer instructions and single-end sequenced for 51 cycles on an Illumina Hi-Seq 2000 or NextSeq 500 per manufacturer instructions. For csRNA-seq, small RNAs of approximately 20–60 nt were size-selected from >1 µg of total RNA with generous spacing on a 15% acrylamide, 7M UREA and 1x TBE gel (Invitrogen EC6885BOX), eluted and precipitated over night at -80°C. Given the RNA fragmentation associated with de-crosslinking, input libraries were generated to eliminate potential false positives and ensure accurate TSS peak calling. csRNA-seq libraries were twice cap selected prior to decapping and libraries were generated as described above. Input libraries were treated with the RppH pyrophosphatase (NEB M0356) prior to adapter ligation to include the whole repertoire of small RNAs with 3’-OH. Samples were quantified by Qbit (Invitrogen). For ChIP-seq, Cells aliquots (500,000) were resuspended on ice in 130 µl RLNR1 lysis buffer (20 mM Tris/HCl pH7.5, 150mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Na-Deoxycholate, 1% NP-40 alternative, 0.5 mM DTT, 1x protease inhibitor cocktail (DTT and protease inhibitors added immediately before use) and transferred to microtubes with an AFA Fiber (Covaris, MA). All subsequent steps were performed on ice or at 4°C. Chromatin was sheared by sonication in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 focused-ultrasonicator (Covaris, MA) for 20 cycles with the following settings: time, 60sec; duty, 5; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun at max speed for 10 mins and the pellet was discarded. 1 % of the sample was stored at -20°C for DNA input control and the remaining supernatant was transferred to PCR strips and brought up to a volume of 200 µl using RLNR1 lysis buffer. For ChIP, 20 μl Protein A/G Dynabeads per sample was washed 2x with 1 ml 0.5% BSA/TE/0.1%Tween20 (TET), resuspended in 0.5% BSA/TET, SREBP antibodies (Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) added, and rotated for 1 hr at RT. The supernatant was removed, Dynabeads washed 1X with 0.1% BSA/TET using a magnet, resuspended in 10 µl RIPA buffer per IP reaction. Dynabeads in RIPA buffer were added to samples and rotated overnight at 4°C. Dynabeads were washed 3 times with Wash Buffer 1 (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), three times with Wash Buffer 3 (10 mM Tris-HCl pH, 250 mM LiCl, 1 mM EDTA, 1% Triton X- 100, 0.7% Na-Deoxycholate) and three times with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween20). Dynabeads were washed once with TE-NaCl (10 mM Tris-HCl pH 8, 1 mM EDTA, 50 mM NaCl) and resuspended in 25 μl TT (10 mM Tris-HCl pH 8, 0.05% Tween20). Input samples were resuspended in 25 μl TT and libraries were generated in parallel with ChIP samples. Library NEBNext End Prep and Adaptor Ligation were performed using NEBNext Ultra II DNA Library Prep kit (New England BioLabs) according to manufacturer instructions using barcoded adapters (NextFlex, Bioo Scientific). Libraries were incubated with RNase A and Proteinase K at 55°C for 1 hour and 65°C overnight. Libraries were PCR amplified for 14 cycles with NEBNext High Fidelity 2X PCR MasterMix (New England BioLabs, NEBM0541). Libraries were size selected for 225 – 350 bp fragments by gel extraction (10% TBE gels, Life Technologies).
Samples were sequenced using the Illumina NextSeq 500 platform using 51 cycles (ChIP-seq) or 75 cycles (csRNA-seq) single-end sequencing per manufacturer instructions. RNA-seq samples were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 (Illumina, San Diego, CA)

treatment_protocol: After monocyte differentiation, on day 7 of culture, moDCs were infected with ZIKV clinical isolate SD001 at MOI 0.5, ZIKV PRVABC59, ZIKV-EGFP-BeH819015 and DENV UIS353 at MOI 1. Briefly, moDCs were incubated 2 hours with the virus, washed with PBS, and incubated in fresh medium for the for 24h at 37˚C, 5% CO2.

tag: donor id

value: monocyte-derived dendritic cell

tag: viral infection

value: ZIKV-infected

tag: viral strain

value: input

tag: time post infection viral infection

tag: experment type


title: RGC439

description: Retinal ganglion cells, scRNA-seq

tag: tissue

value: Retina

value: 7-9 weeks old


title: Mir_16

description: mirVana PARIS kit (Ambion)


title: HEK293_KLF4_K409Q_Input_6

description: HEK293_KLF4_K409Q_Input_6 (biol rep 6)

tag: cell type

value: Human embryonic kidney

value: KLF4 K409Q

value: anti-FLAG M2 (Sigma-Aldrich, #M8823)


title: RGC436

description: Retinal ganglion cells, scRNA-seq


title: Human7_input_ChIPseq_ZIKVnegative_24h

value: ZIKV-bystander


title: Mir_15

description: mirVana PARIS kit (Ambion)

tag: sample type


title: HEK293_KLF4_K409Q_Input_5

description: HEK293_KLF4_K409Q_Input_5 (biol rep 5)


title: RGC438

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: strain


title: HEK293_KLF4_K409Q_Input_4

description: HEK293_KLF4_K409Q_Input_4 (biol rep 4)


title: Mir_14

description: mirVana PARIS kit (Ambion)

value: Implantative endometrium


title: Mir_13

description: mirVana PARIS kit (Ambion)


title: RGC437

description: Retinal ganglion cells, scRNA-seq

tag: age


title: Human7_SREBP_ChIPseq_ZIKVpositive_24h

value: SREBP antibodies (Santa Cruz Biotechnology:sc-8984X, Thermo Fisher Scientific:PA1-337, R&D Systems:AF7119)

value: SREBP ChIP-seq


title: HEK293_KLF4_K409Q_Input_3

description: HEK293_KLF4_K409Q_Input_3 (biol rep 3)


title: Human7_input_ChIPseq_Mock_24h

value: mock infected


title: Human7_SREBP_ChIPseq_ZIKVnegative_24h


title: RGC440

description: Retinal ganglion cells, scRNA-seq


title: Mir_11

description: mirVana PARIS kit (Ambion)

value: Non-implantative endometrium


title: Mir_12

description: mirVana PARIS kit (Ambion)


title: Mir_10

description: mirVana PARIS kit (Ambion)


title: HEK293_KLF4_K409Q_Input_2

description: HEK293_KLF4_K409Q_Input_2 (biol rep 2)


title: RGC444

description: Retinal ganglion cells, scRNA-seq


title: HEK293_KLF4_K409Q_Input_1

description: HEK293_KLF4_K409Q_Input_1 (biol rep 1)


title: Human6_input_ChIPseq_ZIKVpositive_24h


title: RGC445

description: Retinal ganglion cells, scRNA-seq


title: Human6_input_ChIPseq_ZIKVnegative_24h


title: RGC441

description: Retinal ganglion cells, scRNA-seq


title: HEK293_WT_KLF4_IP_6

description: HEK293_WT_KLF4_IP_6 (biol rep 6)

value: WT KLF4


title: RGC442

description: Retinal ganglion cells, scRNA-seq


title: No cells; media only_0_768

organism: synthetic construct

source_name: no cells

value: no cells

tag: chemical

value: No cells; media only

tag: chemical long_name

tag: dose

value: No cells; media only_0

tag: batch

value: Plate 2D index G

tag: sequencing pool

tag: technical control

value: T

tag: reference rna

value: F

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TAGCTCTTC

tag: i5 index_id

value: GGTCTAGCT

tag: cas-rn

tag: iupac name


title: HEK293_WT_KLF4_IP_5

description: HEK293_WT_KLF4_IP_5 (biol rep 5)

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: klf4 genotype

tag: chip antibody

value: anti-FLAG M2 (Sigma-Aldrich, #M8823)


title: HEK293_WT_KLF4_IP_4

description: HEK293_WT_KLF4_IP_4 (biol rep 4)


title: No cells; 1X Lysis buffer_0_767

tag: chemical

value: No cells; 1X Lysis buffer

tag: chemical long_name

tag: treatment

value: No cells; 1X Lysis buffer_0

value: CGTAACTTA


title: RCC-BM2-Normal

tag: condition

value: Normal

tag: Stage

value: ccRCC

value: No

tag: metastasic sites


title: Human6_input_ChIPseq_Mock_24h

tag: donor id

value: monocyte-derived dendritic cell

tag: viral infection

value: mock infected

tag: viral strain

value: input

tag: time post infection viral infection

tag: experment type


title: Human7_SREBP_ChIPseq_Mock_24h

value: SREBP antibodies (Santa Cruz Biotechnology:sc-8984X, Thermo Fisher Scientific:PA1-337, R&D Systems:AF7119)

value: SREBP ChIP-seq


title: RGC410

description: Retinal ganglion cells, scRNA-seq

source_name: Retina

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: No cells; Brain +ve control_0_766

tag: cell line

value: no cells

value: No cells; Brain +ve control

tag: dose

value: No cells; Brain +ve control_0

tag: batch

value: Plate 2D index G

tag: sequencing pool

tag: technical control

value: T

tag: reference rna

tag: solvent control

value: F

tag: well

tag: i7 index_id

tag: index

value: TAGCTCTTC

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn

tag: iupac name


title: RGC443

description: Retinal ganglion cells, scRNA-seq

tag: cell type


title: Nor_11

tag: sample type

value: Endometrial fluid

tag: tissue

value: Non-implantative endometrium


title: Human6_SREBP_ChIPseq_ZIKVnegative_24h

tag: donor id

value: monocyte-derived dendritic cell

tag: viral infection

value: ZIKV-bystander

tag: viral strain

tag: chip antibody

tag: time post infection viral infection

tag: experment type


title: HEK293_WT_KLF4_IP_3

description: HEK293_WT_KLF4_IP_3 (biol rep 3)

tag: cell line

value: Human embryonic kidney

tag: klf4 genotype

value: WT KLF4

value: anti-FLAG M2 (Sigma-Aldrich, #M8823)


title: No cells; Universal human +ve control_0_765

tag: chemical

value: No cells; Universal human +ve control

tag: chemical long_name

tag: dose

tag: treatment

value: No cells; Universal human +ve control_0

tag: batch

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: GATTGTGTT


title: HEK293_WT_KLF4_IP_2

description: HEK293_WT_KLF4_IP_2 (biol rep 2)

tag: cell type


title: Human6_SREBP_ChIPseq_Mock_24h

tag: donor id

tag: viral infection

value: mock infected

tag: viral strain

value: SREBP antibodies (Santa Cruz Biotechnology:sc-8984X, Thermo Fisher Scientific:PA1-337, R&D Systems:AF7119)

value: SREBP ChIP-seq


title: RGC447

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

tag: tissue

value: Retina

tag: strain

tag: age

value: 7-9 weeks old


title: HEK293_WT_KLF4_IP_1

description: HEK293_WT_KLF4_IP_1 (biol rep 1)

tag: cell line

tag: klf4 genotype

tag: chip antibody


title: RGC449

description: Retinal ganglion cells, scRNA-seq


title: Human6_SREBP_ChIPseq_ZIKVpositive_24h

value: ZIKV-infected

tag: time post infection viral infection

tag: experment type


title: RGC448

description: Retinal ganglion cells, scRNA-seq


title: SNU-668 Erastin-resistant cells, shRNA-SOX13 rep2

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome
Fragments per kilobase Million (FPKM) were calculated using the formula:(total exon reads)/[mapped reads(million)*exon length (kb)]
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SNU-668 Erastin-resistant cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SNU-668 Erastin-resistant cells were transfected with shRNA-SOX13 or shRNA-NC

value: gastric cancer cell line

tag: genotype

value: SOX13 knockdown


title: SNU-668 Erastin-resistant cells, shRNA-SOX13 rep3


title: Human5_input_ChIPseq_ZIKVnegative_24h

value: monocyte-derived dendritic cell

value: input


title: RGC446

description: Retinal ganglion cells, scRNA-seq


title: SNU-668 Erastin-resistant cells, shRNA-SOX13 rep1


title: RGC450

description: Retinal ganglion cells, scRNA-seq


title: HEK293_WT_KLF4_Input_5

description: HEK293_WT_KLF4_Input_5 (biol rep 5)

value: Human embryonic kidney


title: Human5_input_ChIPseq_Mock_24h


title: RGC434

description: Retinal ganglion cells, scRNA-seq


title: SNU-668 Erastin-resistant cells, shRNA-NC rep3

value: WT


title: HEK293_WT_KLF4_Input_4

description: HEK293_WT_KLF4_Input_4 (biol rep 4)

value: WT KLF4

value: anti-FLAG M2 (Sigma-Aldrich, #M8823)


title: Human5_SREBP_ChIPseq_ZIKVpositive_24h


title: SNU-668 Erastin-resistant cells, shRNA-NC rep2


title: Human5_input_ChIPseq_ZIKVpositive_24h


title: HEK293_WT_KLF4_Input_3

description: HEK293_WT_KLF4_Input_3 (biol rep 3)


title: Human5_SREBP_ChIPseq_ZIKVnegative_24h

value: ZIKV-bystander


title: HEK293_WT_KLF4_Input_6

description: HEK293_WT_KLF4_Input_6 (biol rep 6)


title: RGC456

description: Retinal ganglion cells, scRNA-seq


title: SNU-668 Erastin-resistant cells, shRNA-NC rep1


title: Mir_7

description: mirVana PARIS kit (Ambion)

tag: sample type

value: Endometrial fluid

value: Implantative endometrium


title: HEK293_WT_KLF4_Input_2

description: HEK293_WT_KLF4_Input_2 (biol rep 2)


title: Human3_csRNAseqinput_ZIKVpos_24h

value: input (csRNA-seq)


title: RGC452

description: Retinal ganglion cells, scRNA-seq


title: HEK293_WT_KLF4_Input_1

description: HEK293_WT_KLF4_Input_1 (biol rep 1)


title: CON_5

tag: subject status

value: health donors

value: blood

tag: treatment

tag: time

value: Day 0


title: RGC458

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina

value: 7-9 weeks old


title: RGC451

description: Retinal ganglion cells, scRNA-seq


title: RGC453

description: Retinal ganglion cells, scRNA-seq


title: Human3_csRNAseqinput_ZIKVneg_24h

tag: donor id


title: 1103W2

city: HEFEI

first: wang

last: hiuru

state: State...

address: NO 17 Lujiang ROAD , HEFEI

department: The First Affiliated Hospital of USTC

institute: USTC

data_processing:
FASTQ files were processed by the 10× Genomics Cell Ranger (3.0.1 version) to map the GRCh38 reference genome and generate a matrix containing normalized gene counts versus cells per sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMCs

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were obtained with informed consent from six patients and isolated from fresh blood collected into EDTA-coated tubes by density gradient centrifugation. Lysis buffer (BD Biosciences) was used to rapidly lyse a small amount of the remaining red blood cells. The cells that passed the test (cell survival rate > 90%) were washed and resuspended to prepare a suitable cell concentration of 800–1100 cells/uL for 10× Genomics ChromiumTM.
Cells were loaded onto the 10× chromium single-cell platform (Single-Cell 3′ library and Gel Bead Kit v.3) and the generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction were all performed according to the manufacturer’s protocol. Qubit was used for library quantification before pooling.
The final library pool was sequenced on the Illumina NovaSeq 6000 system using 150 base-pair paired-end reads.

tag: age(y)

tag: gender

value: male

value: UCBT


title: SEP_2

value: patients with acute sepsis

tag: tissue


title: M2


title: Y8_HaCaT_H3K27ac ChIPseq

city: Houston

first: Yejing

last: Ge

state: Texas

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

description: Sample 9

data_processing:
For Sample 1-6, raw sequencing 150-bp paired-end reads were aligned to the Mus musculus reference genome (version mm10 from Genome Reference Consortium GRCm38) using STAR 2.6.0b aligner. Aligned reads were quantified against the reference annotation (GRCm38) to obtain RPKM (transcripts per million reads) and raw counts using  HTSeq (python/3.6/anaconda3/bin/htseq-count, with options -m union -a 10 -s  no), respectively.
For Sample 7-10, libraries were sequenced using PE150 on a HiSeq4000 lane with about 25-30M reads output per sample and trimmed to obtain SE50 reads and demultiplexed. Raw sequencing 50-bp single-end reads were aligned to the Mus musculus reference genome (version mm10 from Genome Reference Consortium GRCm38) or the Homo sapiens reference genome (version hg19 from Genome Reference Consortium GRCh37) for mouse and human samples, respectively, using the Bowtie (https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.0.1/) pipeline with ( -n 1 -m 1 --best --strata ). Unique reads mapped to a single genomic location (allowing default mismatchesr) were kept for peak identification using the Model based Analysis of Chip-seq 2 (MACS2) (Zhang et al., 2008) pipeline with  parameters ( --nomodel).
For Sample 11, libraries were sequenced using pair end PE150 on a HiSeq4000 lane with about 50M reads output per sample and trimmed to obtain single end SE50 reads and demultiplexed. Raw sequencing 50-bp single end reads were aligned to the genomic builder for Mus musculus (version mm10 from Genome Reference Consortium GRCm38) as previously described (Buenrostro et al., 2013). Briefly, mapping was performed using Bowtie package (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/) with the default parameters. Unique reads mapped to a single genomic location (allowing default mismatches) were kept for peak identification using the Model based Analysis of Chip-seq 2 (MACS2) (Zhang et al., 2008) pipeline with parameters (--nomodel).
Genome_build: hg19 (GRCh37), mm10 (GRCm38)
Supplementary_files_format_and_content: Sample 1-6: *.star.ensembl.htseqcount.gene.txt: tab-delimited text files, gene counts.
Supplementary_files_format_and_content: Sample 7-10: *.macs2_peaks.narrowPeak: bed files, ChIP peaks.
Supplementary_files_format_and_content: Sample 11: *.macs2_peaks.narrowPeak: bed files, ATAC peaks.

source_name: skin

growth_protocol: E17.5 mice skin epithelium or HaCaT cells.

extract_protocol:
For Sample 1-8 and Sample 11, skin was removed and digested with dispase. Then epidermis was peeled from dermis, treated with trypsin and purified based on sort markers indicated.
For Sample 9 and Sample 10, HaCaT cells were treated with trypsin and collected to do ChIP-Seq.
For RNAseq, total RNAs were submitted to Novogene for quality control and polyA enriched eukaryotic mRNA-seq library preparation. For ChIP-Seq and ATAC-Seq, after tagmentation reactions with TnD transposase, libraries that passed QC were then pooled and sequenced.

value: HaCaT

value: immortal keratinocyte cell line

value: wild type

tag: sort markers


title: Human4_RNAseq_ZIKVpositive_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC4_ZIKVpos_RNAseq

value: monocyte-derived dendritic cell

tag: viral infection

value: ZIKV-infected

tag: viral strain

value: Ribosome-depleted RNA-seq


title: Mir_22

description: mirVana PARIS kit (Ambion)

source_name: extracellular vesicles from endometrial fluid

value: Endometrial fluid

value: Non-implantative endometrium


title: RGC459

description: Retinal ganglion cells, scRNA-seq

tag: strain

tag: age


title: Human4_RNAseq_ZIKVnegative_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC4_ZIKVneg_RNAseq

value: ZIKV-bystander

tag: time post infection viral infection


title: Human3_csRNAseqinput_Mock_24h

value: mock infected

tag: experment type

value: input (csRNA-seq)


title: 1102W1


title: Human3_csRNAseq_ZIKVpositive_24h

description:
processed data file: ZIKVpos_csRNAseq_TSS.bed
hDC3_ZIKVpos_csRNAseq

value: capped-small RNA-seq (csRNA-seq)


title: RGC454

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: Human4_RNAseq_Mock_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC4_Mock_RNAseq


title: Y9_HaCaT_KLF5 ChIPseq

description: Sample 10

tag: cell line

tag: genotype

tag: chip antibody


title: Human3_csRNAseq_ZIKVnegative_24h

description:
processed data file: ZIKVneg_csRNAseq_TSS.bed
hDC3_ZIKVneg_csRNAseq


title: C1

value: male

tag: treatment


title: Human3_RNAseq_ZIKVpositive_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC3_ZIKVPos_RNAseq


title: RGC457

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: Human3_csRNAseq_Mock_24h

description:
processed data file: Mock_csRNAseq_TSS.bed
hDC3_Mock_csRNAseq


title: D1

value: UCBT


title: L1

value: female

value: unrelated cord blood transpaltation(UCBT)


title: Human2_csRNAseq_ZIKVpositive_24h

description:
processed data file: ZIKVpos_csRNAseq_TSS.bed
hDC2_ZIKVpos_csRNAseq


title: RGC094

description: Retinal ganglion cells, scRNA-seq


title: Human3_RNAseq_Mock_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC3_Mock_RNAseq


title: Human2_csRNAseq_ZIKVnegative_24h

description:
processed data file: ZIKVneg_csRNAseq_TSS.bed
hDC2_ZIKVneg_csRNAseq


title: RGC099

description: Retinal ganglion cells, scRNA-seq


title: Human2_csRNAseq_Mock_24h

description:
processed data file: Mock_csRNAseq_TSS.bed
hDC2_Mock_csRNAseq


title: Human2_RNAseq_ZIKVnegative_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC2_ZIKVNeg_RNAseq


title: K562.untreated.B1

description: crosslinked MNase-treated nuclei

data_processing:
The SSB site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the exception that additional filter was used: a read-pair was used only if the first base of the read 2 aligned to the genome.
Genome_build: hg19(GRCh37) for human
Supplementary_files_format_and_content: BED files containing coordinates of single-strand breaks

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS, ExCell Bio) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37 °C and 5% CO2.

extract_protocol:
Cells were either crosslinked with formaldehyde in vivo and fragmented with MNase for the standard SSiNGLe-ILM protocol, or directly used for genomic DNA extraction followed by the SSiNGLe on HMW DNA protocol. For SSiNGLe on HMW DNA, the DNA was extracted directly from K562 cells using the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer?s protocol. One hundred nanograms of the DNA was used directly as input into the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) at the polyA-tailing step with only one modification at the Illumina library construction stage. The step 19 in the procedure corresponding to the 2nd round PCR was performed with all (instead of just the 4 µl used in the standard protocol) DNA from the 1st round PCR. The latter was purified with the 2x volume of the VAHTS DNA Clean Beads (Vazyme) before adding to the 2nd round PCR.
The libraries were prepared as described here: https://protocolexchange.researchsquare.com/article/pex-920/v2

treatment_protocol: For drug treatments, three million K562 cells were seeded at 1 million cells per ml of medium per well in 6-well plates. After 16 hr, the cells were separately treated with 0.1% DMSO, 20 ?M Z-DEVD-FMK (AbMole), 100 ?M ICRF-187 (Selleck) and 100 ?M merbarone (Merck) and incubated for 6, 12, 24, 36, or 48 hr. All drugs were dissolved in DMSO, concentration of which was kept at 0.1% in all treatments. Each treatment was done in two independent biological replicas. The cells were used as input in the standard SSiNGLe-ILM protocol on crosslinked nuclei (https://protocolexchange.researchsquare.com/article/pex-920/v2).

value: chronic myelogenous leukemia cell line

value: untreated


title: K562.untreated.B2

description: crosslinked MNase-treated nuclei


title: K562.untreated.B3

description: crosslinked MNase-treated nuclei


title: Human1_csRNAseq_ZIKVpositive_24h

description:
processed data file: ZIKVpos_csRNAseq_TSS.bed
hDC1_ZIKVpos_csRNAseq

value: monocyte-derived dendritic cell

value: ZIKV-infected


title: RGC455

description: Retinal ganglion cells, scRNA-seq


title: RGC100

description: Retinal ganglion cells, scRNA-seq


title: Human2_RNAseq_Mock_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC2_Mock_RNAseq

value: Ribosome-depleted RNA-seq


title: Human3_RNAseq_ZIKVnegative_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC3_ZIKVNeg_RNAseq


title: RGC096

description: Retinal ganglion cells, scRNA-seq


title: Human1_csRNAseq_ZIKVnegative_24h

description:
processed data file: ZIKVneg_csRNAseq_TSS.bed
hDC1_ZIKVneg_csRNAseq


title: Human1_RNAseq_ZIKVpositive_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC1_ZIKVPos_RNAseq


title: Z_DEVD_FMK.48h B4

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 48 hours


title: RGC097

description: Retinal ganglion cells, scRNA-seq


title: Z_DEVD_FMK.36h B4

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 36 hours


title: Human2_RNAseq_ZIKVpositive_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC2_ZIKVPos_RNAseq


title: RGC101

description: Retinal ganglion cells, scRNA-seq


title: Human1_RNAseq_Mock_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC1_Mock_RNAseq

value: mock infected


title: RGC095

description: Retinal ganglion cells, scRNA-seq


title: iDopa/iAstro 1B control, rep2

value: hiPSC-derived midbrain dopaminergic mixed neuronal population (mixture of dopaminergic, glutamatergic, and GABAergic neurons) and astrocytes in co-culture

value: 0.2percent Dimethyl sulfoxide (DMSO) vehicle

value: used to assess expression of specific marker genes

tag: weeks in cutlure before treatment

tag: timepoint

value: 5 hours post DMSO washout


title: RGC098

description: Retinal ganglion cells, scRNA-seq

tag: cell type

value: Retinal ganglion cells

value: Retina


title: Differentiated enterocytes_CmafIECKO_rep2

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
RNA isolated from Epcam+ CD44- sorted cells
AG66f_CmafKOLEC

data_processing:
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 identificatio
Sequencing reads were pseudoaligned using kallisto (v. 0.44.0) against the Mus musculus reference transcriptome obtained from Ensembl (GRCm38.p6). Kallisto was run with default settings plus sequence bias correction.
Transcript level abundances quantified by kallisto were imported into R (v. 3.5.3). Conversion of Ensembl transcript identity to Ensembl gene identity, gene symbols, gene biotype and description was performed using biomaRt (v. 2.38.0).
Counts for gene-level analysis were estimated using the “tximport” function of the tximport package (v. 1.10.0), with abundance estimates scaled using the average transcript length and library size (arguments set to: countsFromAbundance="lengthScaledTPM" and dropInfReps=T).
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: The tab-separated text file contains raw counts per gene per sample as obtained after pseudo-alignment with kallisto, summarized at the gene level with tximport. Counts were rounded to the closest greater integer using ceiling() in R.

source_name: Small intestine tissue

extract_protocol:
Sorted samples were transferred into RLT lysis buffer with β-mercaptoethanol (Qiagen) and snap-frozen on dry ice. RNA was isolated using Qiagen RNeasy Plus Mini Kit (Qiagen). RNA concentration and quality were analysed using 2100 Bioanalyzer (Agilent).
RNA-seq libraries were prepared from 500 ng of total RNA. RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).
Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. 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 (Applied Biosystems, Carlsbad, CA, USA).  USA). After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were 2x150 single-end sequencing using HiSeq 4000 SR, each sample being sequenced on three separate lanes to increase coverage per sample.

treatment_protocol: 4 week old mice received one i.p. injection of  50 μg/g tamoxifen, RNA from sorted cells was isolated from 5 week old mice

value: Epcam+ CD44- enterocytes

value: 5 weeks old

value: CmafIECKO

value: tamoxifen injected

tag: Sex


title: RGC119

description: Retinal ganglion cells, scRNA-seq

value: 7-9 weeks old


title: Differentiated enterocytes_CmafIECKO_rep1

description:
RNA isolated from Epcam+ CD44- sorted cells
AG65f_CmafKOLEC

value: female


title: Human1_RNAseq_ZIKVnegative_24h

description:
processed data file: RNAseq_moDC_ZIKV_24h_FPKM.txt
hDC1_ZIKVNeg_RNAseq

tag: donor id

value: monocyte-derived dendritic cell

value: ZIKV-bystander


title: Z_DEVD_FMK.24h B4

description: crosslinked MNase-treated nuclei

value: chronic myelogenous leukemia cell line

value: treated with Z_DEVD_FMK for 24 hours


title: Z_DEVD_FMK.24h B3

description: crosslinked MNase-treated nuclei


title: Human1_csRNAseq_Mock_24h

description:
processed data file: Mock_csRNAseq_TSS.bed
hDC1_Mock_csRNAseq

value: mock infected

value: capped-small RNA-seq (csRNA-seq)


title: Differentiated enterocytes_WT_ rep3

description:
RNA isolated from Epcam+ CD44- sorted cells
AG63f_WT

tag: tissue

value: wildtype


title: Z_DEVD_FMK.48h B3

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 48 hours


title: RGC120

description: Retinal ganglion cells, scRNA-seq


title: Z_DEVD_FMK.12h B3

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 12 hours


title: Differentiated enterocytes_WT_ rep2

description:
RNA isolated from Epcam+ CD44- sorted cells
AG62f_WT


title: Z_DEVD_FMK.12h B4

description: crosslinked MNase-treated nuclei


title: Differentiated enterocytes_WT_ rep1

description:
RNA isolated from Epcam+ CD44- sorted cells
AG59f_WT


title: Z_DEVD_FMK.06h B4

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 6 hours


title: Z_DEVD_FMK.36h B3

description: crosslinked MNase-treated nuclei

value: treated with Z_DEVD_FMK for 36 hours


title: RGC112

description: Retinal ganglion cells, scRNA-seq

value: Retinal ganglion cells

value: Retina


title: yHN22-ZA-rII-HA_HAvsInput_20170130_Rep1

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

description:
Biological replicate 1 of 2.  ZA-rII'-HA occupancy by ChIP-chip in WT cells. ZA-rII'-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN22-ZA-rII-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_394343

hyb_protocol: ChIP and control samples were combined and dried by SpeedVac. Combined samples were resuspended in 110 µL of fresh hybridization mix (5 µL 10 mg/mL Salmon Sperm DNA (Thermo Fisher Scientific, 15632011), 5 µL 8 mg/mL Yeast tRNA (Thermo Fisher Scientific, 15401011) and 100 µL DIG Easy Hyb (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 45˚C. Samples were hybridized to Agilent microarrays in SureHyb enabled chambers (Agilent, G2534A) with rotation at 42˚C for at least 18 hr. Microarrays were washed on an orbital shaker for 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-Lauroylsarcosine), followed by a second wash with pre-warmed (31˚C) Wash II buffer (0.06X SSPE) for 5 min at room temperature. The microarrays used were described before (Jeronimo and Robert, 2014) and were custom designed by Agilent Technologies and contain a total of about 180,000 Tm-adjusted 60-mer probes covering the entire yeast genome with virtually no gaps between probes.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
bed description: A genome browser-ready file for H2A.Z-HA occupancy by ChIP-chip (H2A.Z/H3) in WT cells.
bed method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP and Input samples were blunted as follow. 40 µL of ChIP DNA or about 400 ng of Input DNA were added to 70 µL of blunting mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples Input DNA or no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: 50 mL of yeast extract peptone (YEP) medium supplemented with 2% galactose was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow at 30°C to an OD600 of 0.6 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 10 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with cold water. Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol: Cell pellets were resuspended in 400 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed using a vortex for 2 hrs at 4C. The lysate was then sonicated 30 cycles, 30 sec ON and 30 sec OFF at High settings (Diagenode Bioruptor). Soluble fragmented chromatin was recovered by centrifugation. 350 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 3.5 μL (1%) were saved as Input sample. 20 μL of Dynabeads coated with protein G pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 200uL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 50°C for 1 hr and subsequently subjected to Proteinase K (5.5 μL 20% SDS, 7.5 μL 10 mg/mL Proteinase K) digestion at 50°C for 1 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: W303a; htz1[delta]::CloNat; bar1[delta]::KANMx; ZA-rII'::HA-URA3

tag: antibody

value: anti-HA (12CA5 from Roche; 2 ug)


title: yHN22-ZA-rII-HA_HAvsInput_20170130_Rep2

description:
Biological replicate 2 of 2.  ZA-rII'-HA occupancy by ChIP-chip in WT cells. ZA-rII'-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN22-ZA-rII-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_394343


title: RGC102

description: Retinal ganglion cells, scRNA-seq

data_processing:
Previously published pipeline STAR version 2.7.0
Assembly: mm10
Supplementary files format and content: Comma-Separated Values files and matrix files

extract_protocol:
The retina is isolated and flat-mounted under dim red light (created with BioRender.com). A retinal ganglion cell is patched and its responses to blue and green spotlight stimuli are recorded. The cell content is aspirated. RNA is processed using Smart-seq2 protocol to get transcriptomic data.
the cDNA library was sequenced on the NovaSeq 6000 instrument and 150-bp paired-end reads were set up. Each sample was sequenced to approximately 10 million reads

value: 7-9 weeks old


title: yHN21-ZA-HA_HAvsInput_20170130_Rep1

description:
Biological replicate 1 of 2.  ZA-HA occupancy by ChIP-chip in WT cells. ZA-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN21-ZA-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_474822

value: W303a; htz1[delta]::CloNat; bar1[delta]::KANMx; ZA::HA-URA3


title: yHN21-ZA-HA_HAvsInput_20170130_Rep2

description:
Biological replicate 2 of 2.  ZA-HA occupancy by ChIP-chip in WT cells. ZA-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN21-ZA-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_474822


title: e6Het_ATACseq

description: Sample 11

value: embryonic skin epithelia

value: wild type

tag: developmental stage

tag: sort markers

value: DAPI-, CD45- and Integrin A6+


title: Z_DEVD_FMK.06h B3

description: crosslinked MNase-treated nuclei

value: chronic myelogenous leukemia cell line


title: YL02_KLF5 ChIPseq

description: Sample 8

tag: strain


title: RGC103

description: Retinal ganglion cells, scRNA-seq

tag: age


title: Merbarone.48h B3

description: crosslinked MNase-treated nuclei

value: treated with Merbarone for 48 hours


title: yHN20-H2A.Z-HA_HAvsInput_20170130_Rep2

description:
Biological replicate 2 of 2.  H2AZ-HA occupancy by ChIP-chip in WT cells. H2AZ-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN20-H2A.Z-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_634316

value: W303a; htz1[delta]::CloNat; bar1[delta]::KANMx; H2AZ::HA-URA3


title: YL01_H3K27ac ChIPseq

description: Sample 7


title: yHN20-H2A.Z-HA_HAvsInput_20170130_Rep1

description:
Biological replicate 1 of 2.  H2AZ-HA occupancy by ChIP-chip in WT cells. H2AZ-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against Input DNA (Cy3-labeled).
SmthBED_yHN20-H2A.Z-HA_HAvsInput_20170130_Rep1-2__S.cerevisiaeApr11_634316


title: RGC113

description: Retinal ganglion cells, scRNA-seq


title: Merbarone.48h B4

description: crosslinked MNase-treated nuclei


title: RGC363

description: Retinal ganglion cells, scRNA-seq


title: yHN22-ZA-rII-HA_HAvsH3_20161220_Rep2

description:
Biological replicate 2 of 2.  ZA-rII'-HA occupancy by ChIP-chip in WT cells. ZA-rII'-HA ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against HA and hybridized against H3 ChIP (Cy3-labeled).
SmthBED_yHN22-ZA-rII-HA_HAvsH3_20161220_Rep1-2__S.cerevisiaeApr11_276022

value: anti-H3 (ab1791 from Abcam; 2 ug)


title: RGC104

description: Retinal ganglion cells, scRNA-seq


title: Merbarone.36h B4

description: crosslinked MNase-treated nuclei

value: treated with Merbarone for 36 hours


title: RGC114

description: Retinal ganglion cells, scRNA-seq


title: Merbarone.36h B3

description: crosslinked MNase-treated nuclei