title: rtgill.dic.1.E10

description:
Library name: rtgill.dic.1.E10
Cell lysate
dic.counts.txt
dic.lib17_S1.E10.expression.values

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: RTgill-W1 dic rep 1 conc 4

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

value: Rainbow trout gill


title: FPE RNA -NR-case 44, miRNA

status: Public on Jan 01 2025

type: RNA

city: Donostia-San Sebastián

first: María

last: Armesto

state: NorthEurope

address: Paseo Dr. Begiristain s/n

department: Molecular Oncology

country: Spain

institute: IIS Biogipuzkoa

description: miRNA expression data from RNA from ccRCC cases

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed in affymetrix TAC (v.4.0.3)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE

label_protocol: standard Affymetrix protocol

growth_protocol: ccRCC were classified as responders and non responders to sunitinib treatment, RNA was extracted from FFPE biopsy material from ccRCC cases

extract_protocol: RNA was extracted from ccRCC cases using the RecoverAll kit according to manufacturers

tag: case

value: case 44

tag: phenotype

value: sunitinib non-responder

tag: tissue

value: ccRCC


title: 43 left start

city: Leuven

first: Johan

last: Van Weyenbergh

address: Herestraat 49

department: DMIT

country: Belgium

institute: KU Leuven

data_processing: Data were normalized for background (negative control probes), internal positive control probes and housekeeping genes using nSolver software version 4.0 (NanoString Technologies, US). Differentially expressed genes and predefined biological pathway scores were determined using nSolver, with correction for multiple testing by the Benjamini-Hochberg method at a 5%  false discovery rate for multiple comparisons cut-off. Comparison of baseline RNA levels for lung side, mechanical ventilation time, donation type and cold ischemia time was done according to the negative binomial distribution with generalized linear models.

source_name: lung biopsy

label_protocol: We did nCounter (NanoString Technologies, US) digital gene expression analysis with the Immunology V2 panel targeting 579 immune system-associated genes. The workflow was carried out as established before in critical COVID-191, fatal COVID-19 nursing home outbreaks2, and respiratory infections at the emergency department3. In short, transcripts -including 15 housekeeping genes - were quantified by hybridization with specific fluorescent barcodes linked to a 50 bp reporter probe and an adjacent 50 bp capture probe.

extract_protocol: Lung tissue biopsy pieces preserved at -80°C were homogenized in Total RNA Lysis Solution (Bio-Rad, Cat#7326820, US) with a 3mm tungsten carbide bead (Qiagen, Cat#69997, Netherlands) using the TissueLyser II (Qiagen, Netherlands). The homogenate underwent RNA extraction with TRIzol (Invitrogen, Cat#15596026, US) and RNA purification with the Aurum Total RNA mini Kit (Bio-Rad, Cat#7326820, US). RNA quality was verified using the NanoPhotometer NP80 Touch (Implen, Germany).

value: left lung

tag: timepoint

value: start donor lung implantation

tag: biopsy set

value: 43 Left

tag: donor age (y)

tag: donor sex

value: male

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: AAV9-DdCBE_5X_rep1 (mouse #25)

type: SRA

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

library_source: transcriptomic

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.3.5) using the parameters:  --species Mmus --cluster-id 0.97 --threads 10 --min-cov 0.0005 --max-mismatches 0.1 --deconv-cov-ratio 0.4 -- max-multi 6 --remap --remap-mismatches 0.075 --crosstalks.
Assembly: mm39
Supplementary files format and content: csv; mim-tRNAseq generated tRNA transcript resad counts
Library strategy: mim-tRNAseq

organism: Mus musculus

source_name: mouse heart tissue

extract_protocol:
Total RNA from either two cell passages of four different cell lines or eight representative hearts from the m.5024T mouse model was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta-elimination (Behrens and Nedialkova, 2022).
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens and Nedialkova, 2022) and sequenced on an Illumina NextSeq 500 platform.

tag: cell type

value: mouse heart tissue


title: rtgill.ampa.3.G09

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.ampa.3.G09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.G09.expression.values

organism: Oncorhynchus mykiss

source_name: RTgill-W1 ampa rep 3 conc 2

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

tag: cell line

tag: treatment


title: 3 right end

tag: tissue

value: right lung

value: end donor lung implantation

value: 3 right

value: hypoxic-ischemic encefalopathy


title: rtgill.ampa.3.F09

description:
Library name: rtgill.ampa.3.F09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.F09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 3


title: 38 right start

tag: timepoint

value: 38 Right

value: female

value: yes


title: AAV9-DdCBE_10X_rep2 (mouse #18)


title: 38 left start

tag: biopsy set

value: 38 Left


title: FPE RNA -R-case 43, miRNA

tag: case

value: case 43

tag: phenotype

value: sunitinib responder

value: ccRCC


title: 37 right start

value: start donor lung implantation

value: 37 Right

tag: donor age (y)

tag: donor sex

tag: donor bmi


title: AAV9-DdCBE_10X_rep1 (mouse #17)


title: FPE RNA -NR-case 102, miRNA

value: case 102

value: sunitinib non-responder


title: FPE RNA -NR-case 33, miRNA

value: case 33


title: rtgill.ampa.3.E09

description:
Library name: rtgill.ampa.3.E09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.E09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 4

value: Rainbow trout gill


title: FPE RNA -NR-case 10, miRNA

value: case 10


title: rtgill.ampa.3.D09

description:
Library name: rtgill.ampa.3.D09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.D09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 5


title: AAV9-GFP_3X_rep2 (mouse #14)

value: mouse heart tissue


title: 37 left start

value: left lung

value: 37 Left

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

value: DCD


title: 36 right start

value: right lung

value: 36 Right

value: female

tag: donor pao2/fio2 ratio

tag: donation type

tag: donor warm ischemia time (min)


title: AAV9-GFP_3X_rep1 (mouse #19)

tag: cell type


title: rtgill.ampa.3.B09

description:
Library name: rtgill.ampa.3.B09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.B09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 7

tag: cell line


title: FPE RNA -R-case 8, miRNA

value: case 8

value: sunitinib responder

value: ccRCC


title: AAV9-GFP_5X_rep1 (mouse #5)


title: 36 left start

value: start donor lung implantation

value: 36 Left

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.ampa.3.C09

description:
Library name: rtgill.ampa.3.C09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.C09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 6

tag: treatment


title: rtgill.ampa.2.H09

description:
Library name: rtgill.ampa.2.H09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.H09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 1


title: FPE RNA -NR-case 2, miRNA

value: case 2

value: sunitinib non-responder

tag: tissue


title: FPE RNA -NR-case 6 , miRNA

tag: case

value: case 6


title: rtgill.ampa.3.A09

description:
Library name: rtgill.ampa.3.A09
Cell lysate
ampa.counts.txt
ampa.lib24_S1.A09.expression.values

source_name: RTgill-W1 ampa rep 3 conc 8

value: Rainbow trout gill


title: AAV9-GFP_5X_rep2 (mouse #6)

value: mouse heart tissue


title: 34 right start

tag: timepoint

tag: biopsy set

value: 34 Right

value: male

value: head trauma


title: MEF_Cl_2_rep2

source_name: mouse embryonic fibroblasts (MEF)

value: mouse embryonic fibroblasts (MEF)


title: 33 right start

value: right lung

value: 33 Right

tag: donor age (y)

tag: donor sex

value: no

value: hypoxic-ischemic encefalopathy

value: DCD


title: MEF_Cl_2_rep1


title: SK-N-DZ Dox IFN 3

city: Memphis

first: Pamela

middle: Morgan

last: Watson

state: Tennessee

address: 71 South Manassas

department: Genetics

country: USA

institute: University of Tennessee Health Science Center

data_processing:
Quantification, differential expression, functional enrichment and novel transcript identification, SNP and InDel analysis, alternative splicing analysis, and fusion gene prediction.
Processed using R DESeq2
Assembly: Human-EukmRNAseq
Supplementary files format and content: tab delimited text file
Supplementary files format and content: tab delimited text file

source_name: neuroectodermal

growth_protocol: SK-N-DZ cells were grown in DMEM during the duration of the study.

extract_protocol:
RNA extraction using Qiagen MiniPrep Kit.
Illumina PE150

treatment_protocol: Cells were treated with doxycycline for four days total, interferon gamma was applied for 24 hours.

value: neuroectodermal

value: SK-N-DZ

value: neuroblastoma

tag: genotype

value: IFN


title: rtgill.ampa.2.G09

description:
Library name: rtgill.ampa.2.G09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.G09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 2


title: 33 left start

value: left lung

value: start donor lung implantation

value: 33 Left

tag: donor bmi

tag: donor smoking history

tag: donor cause of death


title: 31 right start

value: 31 RIght

value: female

value: yes

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD


title: MEF_Cl_1_rep2

tag: cell type

value: mouse embryonic fibroblasts (MEF)


title: SK-N-DZ Dox IFN 2

tag: cell line


title: SK-N-DZ Dox IFN 1


title: MEF_Cl_1_rep1


title: FPE RNA -R-case 9, miRNA

value: case 9

tag: phenotype

value: sunitinib responder

value: ccRCC


title: 31 left start

value: 31 Left

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.ampa.2.D09

description:
Library name: rtgill.ampa.2.D09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.D09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 5

value: Rainbow trout gill

tag: treatment


title: SK-N-DZ IFN 3

tag: tissue

value: neuroectodermal

value: SK-N-DZ

value: WT


title: 30 right start

value: right lung

tag: timepoint

tag: biopsy set

value: 30 Right

tag: donor age (y)

value: no

value: DCD


title: rtgill.ampa.2.C09

description:
Library name: rtgill.ampa.2.C09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.C09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 6


title: MEF_Cl_3_rep2


title: 30 left start

value: left lung

value: start donor lung implantation

value: 30 Left

tag: donor sex

value: female

tag: donor bmi


title: MEF_Cl_3_rep1

value: mouse embryonic fibroblasts (MEF)


title: SK-N-DZ IFN 1

value: neuroblastoma

tag: genotype

value: IFN


title: rtgill.ampa.2.B09

description:
Library name: rtgill.ampa.2.B09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.B09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 7


title: rtgill.ampa.2.A09

description:
Library name: rtgill.ampa.2.A09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.A09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 8


title: SK-N-DZ IFN 2


title: MEF_Ctrl_1_rep1


title: SK-N-DZ Dox 3

value: Control


title: 29 right start

source_name: lung biopsy

value: 29 RIght

tag: donor smoking history

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

value: DBD


title: 29 left start

value: 29 Left

tag: donor pao2/fio2 ratio

tag: donation type


title: rtgill.ampa.2.F09

description:
Library name: rtgill.ampa.2.F09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.F09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 3

tag: cell line

tag: cell type

value: Rainbow trout gill


title: SK-N-DZ Dox 2

value: neuroectodermal

value: SK-N-DZ


title: rtgill.ampa.1.H09

description:
Library name: rtgill.ampa.1.H09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.H09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 1


title: rtgill.ampa.2.E09

description:
Library name: rtgill.ampa.2.E09
Cell lysate
ampa.counts.txt
ampa.lib20_S1.E09.expression.values

source_name: RTgill-W1 ampa rep 2 conc 4


title: rtgill.ampa.1.G09

description:
Library name: rtgill.ampa.1.G09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.G09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 2


title: DRQ-treated DCs 3

city: Rehovot

first: Idit

last: Shachar

address: Herzl

department: Systems Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
fastq files were generated by the usage bcl2fastq-v2.20.0.422 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the Mus musculus genome build GRCm39 using STAR (2.7.3a)
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 has the UMI)
Reads were counted using Ensembl annotations, build 106 (1000 bases of the 3’ UTR), using HTSeq-Counts (version 0.11.2), and corrected for UMI saturation
Normalization and differential expression analysis were performed using DESeq2 (1.26.0)
Assembly: GRCm39
Supplementary files format and content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary files format and content: Excel file includes the normalized counts (DESeq Normalization)

molecule: polyA RNA

source_name: breast cancer

extract_protocol:
RNA was harvesed using Dynabeads kit (quiagen)
A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019)
RNA-Seq (3') UMI appears in Read2

value: breast cancer

value: DCs

value: WT

value: DRQ


title: DRQ-treated DCs 4


title: SK-N-DZ Dox 1


title: MEF_Ctrl_1_rep2


title: DRQ-treated DCs 2


title: SK-N-DZ Control 3


title: 28 left start

value: left lung

value: start donor lung implantation

value: 28 Left

value: no

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: rtgill.ampa.1.E09

description:
Library name: rtgill.ampa.1.E09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.E09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 4

tag: treatment


title: 27 right start

tag: tissue

value: right lung

value: 27 right

value: male

value: head trauma

tag: cold ischemia (min)


title: DRQ-treated DCs 1


title: 27 left start

tag: timepoint

tag: biopsy set

value: 27 left

value: DBD


title: rtgill.ampa.1.C09

description:
Library name: rtgill.ampa.1.C09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.C09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 6

value: Rainbow trout gill


title: PBS-treated DCs 3

value: PBS


title: SK-N-DZ Control 1

value: neuroectodermal

value: SK-N-DZ

value: neuroblastoma

value: Control


title: rtgill.ampa.1.D09

description:
Library name: rtgill.ampa.1.D09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.D09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 5


title: PBS-treated DCs 4

value: breast cancer

value: DCs

value: WT


title: 22 year, BR, rep2

city: Guangzhou

first: Yicong

last: Xu

state: Guangdong

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-98333-12

library_source: transcriptomic single cell

data_processing:
Sequence alignment was based on the rheMac10 genome.
The overall processing with umi and barcode were performed by CellRanger software.
The raw expression data was scaled and normalized using the regularized negative binomial regression by sctransform package.
Assembly: rheMac10
Supplementary files format and content: Tab-separated matrix files of counts for all samples
Supplementary files format and content: Tab-separated matrix files of sample information

organism: Macaca mulatta

source_name: Testicle

extract_protocol:
The testicular tissue of macaque was washed with PBS solution, stripping off the albuginea white and cut into pieces. The tissue pieces were then incubated in 5% Type IV collagenase. After washing twice in PBS. 10% fetal bovine serum was added to finish digestion, and the cell suspension was centrifuged to remove the supernatant.
The isolated cells were contained in GEM, and poly-A RNA of cells was amplified. The final transcriptome library was built as the protocol of 10x single cell 3’ v2.

value: Testis cell

value: Testicle

tag: strain

value: Normal

tag: age

value: 22 years old


title: 26 right start

value: right lung

value: start donor lung implantation

value: 26 right

tag: donor age (y)

tag: donor sex

value: female

tag: donor bmi

value: yes

value: intracranial bleeding


title: 26 left start

value: left lung

value: 26 left

tag: donor smoking history

tag: donor cause of death

tag: donor mechanical ventilation (hours)

value: DBD


title: 28 right start

value: 28 Right

value: no

value: hypoxic-ischemic encefalopathy

tag: donor pao2/fio2 ratio

tag: donation type


title: rtgill.ampa.1.B09

description:
Library name: rtgill.ampa.1.B09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.B09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 7

tag: cell line

tag: cell type

value: Rainbow trout gill


title: PBS-treated DCs 2

value: breast cancer

value: DCs

tag: genotype

value: WT

tag: treatment

value: PBS


title: 22 year, BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-98093-12

value: Testis cell

tag: tissue

value: Testicle

value: Normal

value: 22 years old


title: 25 right start

value: right lung

tag: timepoint

value: start donor lung implantation

value: 25 right

value: female

value: yes

value: DCD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: rtgill.ampa.1.A09

description:
Library name: rtgill.ampa.1.A09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.A09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 8


title: PBS-treated DCs 1


title: 1 year, BR, rep2

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-197007-12

tag: strain

tag: age

value: 1 year old


title: rtgill.ampa.1.F09

description:
Library name: rtgill.ampa.1.F09
Cell lysate
ampa.counts.txt
ampa.lib16_S1.F09.expression.values

source_name: RTgill-W1 ampa rep 1 conc 3


title: 25 left start

value: left lung

tag: biopsy set

value: 25 left

tag: donor age (y)

tag: donor sex

tag: donor bmi

value: hypoxic-ischemic encefalopathy


title: rtgill.car.3.H08

description:
Library name: rtgill.car.3.H08
Cell lysate
car.counts.txt
car.lib24_S1.H08.expression.values

source_name: RTgill-W1 car rep 3 conc 1

value: Rainbow trout gill


title: 1 year, BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-195041-12


title: Fasted rep4

city: Shanghai

first: Mingyang

last: Yuan

address: No. 573, Xujiahui Road, Huangpu District

institute: Shanghai Institute of Endocrine and Metabolic Diseases

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software 1.14
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Assembly: GRCm38
Supplementary files format and content: Microsoft excel file includes the Read Counts miRNAs in all samples.

source_name: the arcuate nucleus of the hypothalamus

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: the arcuate nucleus of the hypothalamus


title: 23 left start

value: 23 left

value: male

tag: donor smoking history

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DBD


title: rtgill.car.3.G08

description:
Library name: rtgill.car.3.G08
Cell lysate
car.counts.txt
car.lib24_S1.G08.expression.values

source_name: RTgill-W1 car rep 3 conc 2

tag: cell line

tag: cell type


title: SK-N-DZ Control 2

source_name: neuroectodermal

tag: tissue

value: neuroectodermal

value: SK-N-DZ

value: neuroblastoma

tag: genotype

value: WT

tag: treatment

value: Control


title: Fasted rep3


title: 6 year, BR, rep2

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-146057-12

value: Testis cell

value: Testicle

value: Normal

value: 6 years old


title: 22 right start

source_name: lung biopsy

value: right lung

tag: timepoint

value: start donor lung implantation

value: 22 right

value: no

value: ischemic stroke

tag: donation type

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: 22 left start

value: left lung

tag: biopsy set

value: 22 left

value: male

tag: cold ischemia (min)


title: 6 year, BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-145269-12

tag: strain

tag: age


title: Fasted rep1

value: the arcuate nucleus of the hypothalamus


title: 22 year, Non-BR, rep2

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-98333

value: 22 years old


title: 21 right start

value: 21 right

tag: donor age (y)

tag: donor sex

tag: donor bmi

tag: donor smoking history

value: hypoxic-ischemic encefalopathy

value: DCD


title: Control rep3


title: rtgill.car.3.D08

description:
Library name: rtgill.car.3.D08
Cell lysate
car.counts.txt
car.lib24_S1.D08.expression.values

source_name: RTgill-W1 car rep 3 conc 5

tag: cell line

value: Rainbow trout gill


title: 22 year, Non-BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-98093

tag: cell type

value: Testis cell

value: Testicle


title: Control rep2

tag: tissue


title: Control rep1


title: rtgill.car.3.C08

description:
Library name: rtgill.car.3.C08
Cell lysate
car.counts.txt
car.lib24_S1.C08.expression.values

source_name: RTgill-W1 car rep 3 conc 6


title: 20 right start

value: 20 right

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio


title: 6 year, Non-BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-145269

value: Normal

value: 6 years old


title: 6 year, Non-BR, rep2

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-146057


title: rtgill.car.3.B08

description:
Library name: rtgill.car.3.B08
Cell lysate
car.counts.txt
car.lib24_S1.B08.expression.values

source_name: RTgill-W1 car rep 3 conc 7

tag: treatment


title: 20 left start

tag: timepoint

value: start donor lung implantation

value: 20 left

tag: donation type

tag: donor warm ischemia time (min)


title: Sample_pre_n4

city: Montreal

first: Alyson

last: Fournier

state: QC

address: 3801 Rue University

department: Department of Neurology and Neurosurgery

data_processing:
Sequences were demultiplexed with 0 mismatches using bcl2fast1 2.20
Reads were trimmed with cutadapt
Reads were aligned with hisat2
Count matrices were generated by htseq
DESeq2 was used for count normalization and differential gene expression analysis
Assembly: not provided
Supplementary files format and content: RNA_Metadata_EAE_RGC.xlsx

source_name: Eyes

extract_protocol: Total RNA extraction was performed using the Qiagen miRNeasy kit according to manufacturer recommendations.

value: Eyes

value: Retinal ganglion cell neurons (RGCs)

value: 7-8 weeks

tag: Sex

value: female

value: EAE

tag: Stage

value: pre


title: rtgill.car.2.H08

description:
Library name: rtgill.car.2.H08
Cell lysate
car.counts.txt
car.lib20_S1.H08.expression.values

source_name: RTgill-W1 car rep 2 conc 1


title: rtgill.car.3.F08

description:
Library name: rtgill.car.3.F08
Cell lysate
car.counts.txt
car.lib24_S1.F08.expression.values

source_name: RTgill-W1 car rep 3 conc 3


title: Sample_pre_n3

tag: age


title: 1 year, Non-BR, rep1

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-195041

tag: strain

value: 1 year old


title: 1 year, Non-BR, rep2

description:
Single-cell samples dissociated from fresh testicular tissue
RNA-197007


title: rtgill.car.3.A08

description:
Library name: rtgill.car.3.A08
Cell lysate
car.counts.txt
car.lib24_S1.A08.expression.values

source_name: RTgill-W1 car rep 3 conc 8


title: 16 left start

value: left lung

tag: biopsy set

value: 16 left

tag: donor age (y)

tag: donor sex

value: yes

value: intracranial bleeding

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: 16 right start

tag: tissue

value: right lung

value: 16 right

tag: donor bmi

tag: donor smoking history

value: DCD


title: 15 right start

value: 15 right

value: male

value: no

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DBD


title: Fasted rep2

value: the arcuate nucleus of the hypothalamus


title: 15 left start

tag: timepoint

value: start donor lung implantation

value: 15 left

tag: donation type


title: Sample_pre_n2

value: Eyes

tag: cell type

value: Retinal ganglion cell neurons (RGCs)

value: 7-8 weeks

tag: Sex

value: female

tag: treatment

value: EAE


title: rtgill.car.2.E08

description:
Library name: rtgill.car.2.E08
Cell lysate
car.counts.txt
car.lib20_S1.E08.expression.values

source_name: RTgill-W1 car rep 2 conc 4

tag: cell line

value: Rainbow trout gill


title: rtgill.car.2.G08

description:
Library name: rtgill.car.2.G08
Cell lysate
car.counts.txt
car.lib20_S1.G08.expression.values

source_name: RTgill-W1 car rep 2 conc 2


title: rtgill.car.2.F08

description:
Library name: rtgill.car.2.F08
Cell lysate
car.counts.txt
car.lib20_S1.F08.expression.values

source_name: RTgill-W1 car rep 2 conc 3


title: 14 right start

tag: biopsy set

value: 14 right

value: yes

value: hypoxic-ischemic encefalopathy

tag: donor warm ischemia time (min)


title: 14 left start

value: left lung

value: 14 left

tag: donor age (y)

tag: donor sex


title: Sample_onset_n4

tag: age

tag: Stage

value: onset


title: Sample_pre_n1

tag: tissue

value: pre


title: 12 right start

value: right lung

value: 12 right

tag: donor bmi

tag: donor smoking history

value: no

value: DBD

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: 11 left start

tag: timepoint

value: start donor lung implantation

value: 11 left

value: male

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

value: DCD


title: 12 left start

value: 12 left

value: female

tag: donation type


title: 11 right start

value: 11 right


title: Sample_peak_n2

value: Eyes

tag: cell type

value: Retinal ganglion cell neurons (RGCs)

value: 7-8 weeks

tag: Sex

tag: treatment

value: EAE

value: peak


title: rtgill.car.2.D08

description:
Library name: rtgill.car.2.D08
Cell lysate
car.counts.txt
car.lib20_S1.D08.expression.values

source_name: RTgill-W1 car rep 2 conc 5

tag: cell line

value: Rainbow trout gill


title: rtgill.car.2.A08

description:
Library name: rtgill.car.2.A08
Cell lysate
car.counts.txt
car.lib20_S1.A08.expression.values

source_name: RTgill-W1 car rep 2 conc 8


title: rtgill.car.2.C08

description:
Library name: rtgill.car.2.C08
Cell lysate
car.counts.txt
car.lib20_S1.C08.expression.values

source_name: RTgill-W1 car rep 2 conc 6


title: Sample_peak_n1


title: rtgill.car.2.B08

description:
Library name: rtgill.car.2.B08
Cell lysate
car.counts.txt
car.lib20_S1.B08.expression.values

source_name: RTgill-W1 car rep 2 conc 7


title: Sinorhizobium meliloti AD005 IPTG, Replicate 2

city: Stanford

first: Sharon

middle: R

last: Long

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

hyb_protocol: Four micrograms of fragmented, labeled cDNA was hybridized to a custom GeneChip at 48 degree celsius for 16 hours as described in Barnett et al 2004. GeneChips were washed and stained using a modified ProkGE-WS2v3-450 fluidics protocol.

scan_protocol: GeneChips were scanned at the Stanford PAN facility using an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; lob base 2 transformation; median polish summarization

organism: Sinorhizobium meliloti

source_name: CL150 ΔbamA pSRKKm_bamA, BamA expressed off of IPTG-inducible promoter (control)

label_protocol: cDNA was fragmented and biotin-labeled as described in Barnett et al 2004.

growth_protocol: Prepared 20mL samples in LB medium at a starting OD600 of 0.3 in 125 mL baffled flasks. Cultures were grown at 30̊C with constant shaking at 250 rpm for 4 hours to a target OD600 of 0.5-0.7. Samples were spun down with 5% buffer-equilibrated phenol in ethanol at 4̊̊C and then flash-frozen.

extract_protocol: RNA was extracted from cells using a modified RNeasy protocol (described in Barnet et al 2004; PNAS), and cDNA was synthesized from extracted RNA using SuperScript III reverse transcriptase

treatment_protocol: Control samples were grown with 1mM IPTG, resulting in sustained BamA expression. Washout samples were grown with no IPTG, resulting in depletion of BamA.

tag: strain


title: Sinorhizobium meliloti AD005 IPTG, Replicate 1


title: rtgill.car.3.E08

description:
Library name: rtgill.car.3.E08
Cell lysate
car.counts.txt
car.lib24_S1.E08.expression.values

source_name: RTgill-W1 car rep 3 conc 4


title: Sample_onset_n3

tag: age

value: onset


title: Sinorhizobium meliloti AD005 Washout, Replicate 1

source_name: CL150 ΔbamA pSRKKm_bamA, no BamA expression


title: Sample_onset_n2

tag: Stage


title: 10 right start

source_name: lung biopsy

tag: tissue

value: right lung

tag: biopsy set

value: 10 right

tag: donor age (y)

tag: donor sex

value: hypoxic-ischemic encefalopathy

tag: donor warm ischemia time (min)


title: sgs3,Rep3

city: Hangzhou

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University

description:
Library name: sgs33
Illumina HiSeqTM2000

data_processing:
The clean reads were mapped to the reference genome of Nipponbare (MSU7.v7.0) using the Bowtie 2 (Cock et al. 2010; Langmead et al. 2009) in HISAT2 version 2.1.0 (Kim et al. 2015)
The isoforms of the same gene were decided using the RSEM software (Li and Dewey 2011). The transcript abundance was measured in terms of Transcripts Per Million (TPM) in the StringTie software.
Gene co-expression analysis was carried out using WGCNA.
Deseq2 (version 1.12.4) was used for differentially expressed gene (DEG) analysis with q-value < 0.001 and |Fold Change| > 2.
Assembly: MSU;  Reference genome source: http://rice.plantbiology.msu.edu/index.shtml? ;The sequence alignment between the Clean Reads of each sample and the designated reference genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: Grains

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Grains

value: Grain cells

tag: genotype

value: mutant

value: EMS Treatment

tag: batch

value: total RNA


title: Sinorhizobium meliloti AD005 IPTG, Replicate 3


title: Sinorhizobium meliloti AD005 Washout, Replicate 2


title: Sinorhizobium meliloti AD005 Washout, Replicate 3


title: Sample_naive_n5

value: female

value: Control

value: naive


title: sgs3,Rep2

description:
Library name: sgs32
Illumina HiSeqTM2000


title: rtgill.car.1.G08

description:
Library name: rtgill.car.1.G08
Cell lysate
car.counts.txt
car.lib16_S1.G08.expression.values

source_name: RTgill-W1 car rep 1 conc 2


title: rtgill.car.1.F08

description:
Library name: rtgill.car.1.F08
Cell lysate
car.counts.txt
car.lib16_S1.F08.expression.values

source_name: RTgill-W1 car rep 1 conc 3


title: Sample_naive_n4

source_name: Eyes

value: Eyes

value: Retinal ganglion cell neurons (RGCs)


title: rtgill.car.1.H08

description:
Library name: rtgill.car.1.H08
Cell lysate
car.counts.txt
car.lib16_S1.H08.expression.values

source_name: RTgill-W1 car rep 1 conc 1


title: Zhenong 34,Rep3

description:
Library name: WT3
Illumina HiSeqTM2000

value: Wild type


title: 9 right start

tag: timepoint

value: start donor lung implantation

value: 9 right

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: head trauma

tag: donor mechanical ventilation (hours)

value: DBD

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: Sample_onset_n1

tag: cell type

value: 7-8 weeks

tag: Sex

tag: treatment

value: EAE

value: onset


title: Sample_naive_n2

tag: tissue

tag: age

tag: Stage


title: 9 left start

value: left lung

tag: biopsy set

value: 9 left

tag: donor age (y)

tag: donor sex

tag: donor pao2/fio2 ratio

tag: donation type


title: taVNS-2

city: CHANGSHA

first: Zhendong

last: LI

address: Changsha, Hunan Province

institute: Hunan University of Chinese Medicine

data_processing:
quality control is performed to remove possible adapter sequences and nucleotides with poor quality using SOAPnuke(v1.5.2)
the filtered clean reads were mapped to the Rattus_norvegicus reference genome (version: GCF_015227675.2_mRatBN7.2) using the HISAT (v2.0.4) andBowtie2 (v2.2.5)
performed gene quantification analysis using RSEM (v1.2.8)
performed Pearson correlation analysis, and principal component analysis (PCA) using R
The DEGseq method based on the negative binomial distribution principle was used to screen differentially expressed genes
Assembly: Rattus_norvegicus reference genome (version: GCF_015227675.2_mRatBN7.2)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM value for each sample

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
50 mg hippocampal tissue from each mouse was homogenized in 1 ml of Trizol reagent (Cat # 15596026, THERMO) using a glass tissue homogenizer. Phase separation of Trizol homogenate using chloroform, followed by RNA extraction using an RNA analysis kit according to the manufacturer's instructions (Cat # DNF-471, AATI). RNA Intergrity (RIN) was confirmed via Fragment Analyzer 7100 (AATI) and samples with 28S/18S≥0.7 and RIN≥7 were selected for the next experiment.
Oligo dT Selection to enrich the mRNA; RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); End repair, add A and adaptor ligation; PCR; circularization and make DNA Nanoball

treatment_protocol: Rats with both spontaneous alternation rate and cognitive index lower than 20% of the mean value of the control group were included in the experiment and randomly divided into the PSCI group and the taVNS group. The control and PSCI groups were fed routinely, while the taVNS group underwent a 14-day transcutaneous auricular vagus nerve stimulation.

value: hippocampus

tag: gender

value: male

value: Cognitive impairment after MACO, with taVNS intervention for 2 weeks


title: Sample_naive_n1

value: female

value: Control

value: naive


title: 10 left start

tag: timepoint

value: 10 left

tag: donor bmi

tag: donor smoking history

value: hypoxic-ischemic encefalopathy

value: DCD

tag: donor warm ischemia time (min)


title: 8 left start

value: start donor lung implantation

value: 8 left

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: Zhenong 34,Rep1

description:
Library name: WT1
Illumina HiSeqTM2000

tag: tissue

value: Grains

tag: cell type

value: Grain cells

tag: genotype

value: Wild type

tag: treatment

tag: batch

value: total RNA


title: Onset_3

library_source: genomic

data_processing:
Sequences were demultiplexed with 0 mismatches using bcl2fast1 2.20
Reads were trimmed with cutadapt
Reads were aligned with hisat2
Count matrices were generated by htseq
TSS quantification

molecule: genomic DNA

extract_protocol:
Approximately 15 to 50 thousand cells were pelleted after FACS isolation by centrifuging at 500g for 5 minutes at 4°C. The pellet was carefully resuspended in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), then immediately centrifuged at 4°C, 500g, for 10 minutes. The supernatant was pipetted off, and the pellet was resuspended in 50 uL of transposition buffer (25 uL Tagment DNA Buffer, 2.5 uL Tagment DNA enzyme 1, 22.5 uL nuclease free H2O) and incubated at 37°C for 30 minutes. After transposition, DNA was isolated using the Zymo ChIP DNA Clean & Concentrator Kit per manufacturers instructions, and eluted in 11 uL of 10 mM Tris Buffer, pH 8.0.
Library preparation was done using Nextera primer sequences and NEB Next High Fidelity 2X PCR master mix (M0541L) and amplification was run for 10 cycles.

value: Eyes

tag: Sex

value: Retinal ganglion cell neurons (RGCs)

tag: disease stage

value: Onset

value: EAE


title: sgs3,Rep1

description:
Library name: sgs31
Illumina HiSeqTM2000

value: mutant

value: EMS Treatment


title: 8 right start

value: right lung

tag: biopsy set

value: 8 right

tag: donor age (y)

tag: donor sex

value: male

tag: donor pao2/fio2 ratio

tag: donation type

value: DBD


title: taVNS-1

value: hippocampus

tag: gender

value: Cognitive impairment after MACO, with taVNS intervention for 2 weeks


title: PSCI-3

value: Cognitive impairment after MCAO, with regular feeding for 2 weeks


title: Peak_4

value: female

value: Peak


title: 7 right start

tag: timepoint

value: start donor lung implantation

value: 7 right

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor warm ischemia time (min)


title: Presymptomatic_4

tag: tissue

value: Eyes

tag: cell type

value: Retinal ganglion cell neurons (RGCs)

value: Presymptomatic


title: 7 left start

value: left lung

value: 7 left

tag: donor mechanical ventilation (hours)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: PSCI-1

tag: treatment


title: Peak_3

tag: Sex

tag: disease stage

value: EAE


title: Peak_2


title: taVNS-3

value: male


title: 5 left start

tag: biopsy set

value: 5 left

tag: donor age (y)

tag: donor sex

value: head trauma

value: DBD


title: Zhenong 34,Rep2

description:
Library name: WT2
Illumina HiSeqTM2000

value: Grains

value: Grain cells

tag: genotype

value: Wild type

value: Control

tag: batch

value: total RNA


title: Peak_1

value: female

value: Peak


title: control-2

value: hippocampus

tag: gender

value: Regular feeding


title: 4 right start

value: right lung

tag: timepoint

value: start donor lung implantation

value: 4 right

tag: donor bmi

tag: donor smoking history

value: no

value: hypoxic-ischemic encefalopathy

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD


title: PSCI-2

tag: tissue

value: male

value: Cognitive impairment after MCAO, with regular feeding for 2 weeks


title: 4 left start

value: left lung

value: 4 left

tag: donor cause of death

tag: donor mechanical ventilation (hours)

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)


title: control-1

tag: treatment


title: Onset_2

value: Eyes

tag: Sex

tag: cell type

value: Retinal ganglion cell neurons (RGCs)

tag: disease stage

value: Onset

value: EAE


title: Onset_1

value: female


title: Pj_L3s_egg_mRNA

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description: Pj

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter(GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG) trimmed with fastx_clipper
mapped using bowtie -t -k 2 -v 2 -p 16 --sam --quiet  --solexa1.3-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
detecting different expression gene using edgeR
Genome_build: Final_unigene.fa (Parabronema skrjabini denovo transcriptome assembly)
Supplementary_files_format_and_content: expressed_gene_RPKM.txt reports abundance measurements

organism: Parabronema skrjabini

source_name: third-stage larvae

extract_protocol:
Total RNA was extracted from eggs, infective larvae, adult male and female using the TRIzol reagent. RQ1 DNase was added to remove the DNA templates. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smart spec plus. RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each stage, 5μg of total RNA was used for RNA-seq library preparation with the Balancer NGS Library Preparation Kit (Gnomegen). Dyna oligo (dT) beads (Ambion) were used to isolated poly(A) mRNA from the total RNA samples. Purified mRNAs were fragmented into short pieces in fragmentation buffer. RNA fragments were end-repaired and ligated with 5'adaptor. Then reverse transcription was performed using RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. The PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 ℃ until used for sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to Illumina Nextseq 500 system for 150nt and Hiseq 2000 system for 90nt paired-end sequencing by ABlife. Inc (Wuhan, China).

tag: developmental stage


title: Presymptomatic_3

value: Presymptomatic


title: 3 right start

tag: biopsy set

value: 3 right

tag: donor age (y)

tag: donor sex

tag: cold ischemia (min)


title: 2 right start

value: right lung

tag: timepoint

value: 2 right

tag: donor bmi

tag: donor smoking history

value: intracranial bleeding


title: Presymptomatic_2

tag: tissue


title: N2 young adult on E. coli OP50  rep3

city: Taipei

first: Yi-Chun

last: Wu

address: No. 1, Sec. 4, Roosevelt Rd.,

country: Taiwan

institute: National Taiwan University

data_processing:
The sequencing data were converted from base call files to FASTQ files using Illumina’s bcl2fastq v2.2.0. The raw FASTQ files were first processed with Trimmomatic v0.3966 for adaptor trimming and quality control. The C. elegans genomic reference sequence WBcel235/ce11 was downloaded from Wormbase72, and the gene annotation file (release 100) was downloaded from Ensembl73. The paired-end reads were aligned and mapped to C. elegans genomic reference sequence using HISAT2 v2.2.074, followed by quantifying the raw read counts of individual genes using featureCounts v2.0.175. The differential expression between different diet-fed worms was statistically assessed using the R/Bioconductor package DESeq2 v1.28.176.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited txt file includes counts (tpm) for each sample

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
RNA was extracted using TRIzol following the manufacturer’s protocol. 1 ug of total RNA was used for the construction of sequencing library.
The RNA-seq libraries were prepared using the Illumina TruSeq® Stranded mRNA kit according to the manufacturer’s protocol starting with 1 μg total RNA.

value: whole worm

tag: genotype

value: wild-type

value: feeding OP50


title: Twist2-Cre/A20fl/fl liver

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

source_name: CKO

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

value: liver


title: N2 young adult on E. coli OP50  rep2


title: N2 young adult on E. coli OP50  rep1


title: 3 left start

value: start donor lung implantation

value: 3 left

value: male

value: no

tag: donor cause of death

value: hypoxic-ischemic encefalopathy

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type

value: DCD


title: HCC biopsy 6_response

city: London

first: Rohini

last: Sharma

state: London

address: Du Cane Road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: NanoString technology uses a unique system of color-coded probes to capture and count specific RNA molecules without the need for amplification.

scan_protocol: The aligned complexes were imaged, and the specific order of fluorescent signals in each barcode was used to identify and quantify the target RNA

data_processing: The nCounter Human Immunology V2 Panel includes 579 genes covering the core pathways and processes of the immune response, and 15 internal reference genes for data normalization.

source_name: Liver Tissue

label_protocol: Approximately 50 base pairs long and is complementary to the target RNA sequence. It was coupled to a biotin tag, which allows for immobilization of the target-probe complex

extract_protocol: RNA was purified from samples using Allprep DNA/RNA mini kit (Qiagen, Venlo, NL, Cat. 80234).

tag: age

value: Imperial College London

value: United Kingdom

tag: Sex

value: HCC biopsy


title: FS-887 [CD4]

type: genomic

city: Moscow

first: Ivan

middle: S

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Methylation data processing and normalization were performed using ChAMP R package. Probes with detection p-value above 0.01, multi-hit probes, probes close to SNPs and non-autosomal probes were filtered out from the subsequent analysis using champ.filter() function with default parameters. A beta-mixture quantile normalization method (BMIQ) provided by champ.norm() function was used to normalize methylation data for probe type bias.

label: CD4 MicroBeads, human (Miltenyi Biotec)

source_name: CD4+ T lymphocytes

label_protocol: Standard Illumina protocol

extract_protocol: Cells were extracted using CD4 microbeads (Miltenyi Biotec). DNA was prepared using QIAamp DNA Mini Kit (Qiagen)

tag: subject status

value: treatment-naïve patients with multiple sclerosis in relapse

tag: group

value: female

tag: cell type

value: CD4+ T lymphocytes


title: N2 young adult on Comamonas DA1877 rep3

tag: treatment

value: feeding DA1877


title: Twist2-Cre liver

source_name: Control


title: Naïve_5

value: Eyes

value: Retinal ganglion cell neurons (RGCs)

tag: disease stage

value: Control


title: control-3

value: hippocampus

tag: gender

value: Regular feeding


title: FS-796 [CD4]


title: HCC biopsy 4_nonresponse


title: 1 left start

value: left lung

tag: timepoint

value: start donor lung implantation

tag: biopsy set

value: 1 left

tag: donor age (y)

tag: donor sex

value: yes

value: DBD

tag: donor warm ischemia time (min)

tag: biopsy rewarming ischemia time (min)

tag: cold ischemia (min)


title: HCC biopsy 5_nonresponse

value: Imperial College London

value: male

tag: tissue


title: FS-881 [CD4]


title: Naïve_3


title: Presymptomatic_1

value: Presymptomatic

value: EAE


title: N2 young adult on Comamonas DA1877 rep2

value: whole worm

tag: genotype

value: wild-type


title: 6 right start

value: right lung

value: 6 right

tag: donor bmi

tag: donor smoking history

value: no

tag: donor cause of death

value: intracranial bleeding

tag: donor mechanical ventilation (hours)

tag: donor pao2/fio2 ratio

tag: donation type


title: FS-884 [CD4]

tag: subject status

value: treatment-naïve patients with multiple sclerosis in relapse

tag: group

tag: age

tag: Sex

value: female

tag: cell type

value: CD4+ T lymphocytes


title: HCC biopsy 3_response

value: United Kingdom

value: HCC biopsy


title: Naïve_4

value: Eyes

value: Retinal ganglion cell neurons (RGCs)

tag: disease stage

tag: treatment

value: Control


title: FS-795 [CD4]


title: FS-880 [CD4]

value: male


title: Naïve_2


title: N2 young adult on Comamonas DA1877 rep1

value: feeding DA1877


title: sorted T cells from 4 patients including 2 patients with influenza_#1and#3

status: Public on Dec 30 2024

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

description: Library name: actTcells_all_GEX

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.h5 files containing the information needed to evaluate date in R using Seurat (e.g.)
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files containing the B-cell receptor informations for the samples.

source_name: sorted activated T cells from peripheral blood

extract_protocol:
Frozen PBMC from 11 MIS-C patients and from 4 patients who were 6 weeks post-infection with SARS-CoV-2 without developing MIS-C were thawed in RPMI 1640 with 20%v/v FCS. Cells were washed once in PBS containing 1%w/v BSA, 2mM EDTA and 2µg/ml Actinomycin D. Cells were incubated with human FcR blocking reagent and stained for 30 min at 4°C with fluorophore-coupled anti-human antibodies. Simultaneously, cells were incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). DAPI was added before sorting to allow dead cell exclusion. Activated T cells were identified as DAPI-, CD14-, CD19-, CD3+, CD38+ and HLA-DRhigh, memory B cells were identified as DAPI-, CD14-, CD3-, CD19+, CD27+ (and CD38high for plasmablasts), and monocytes were identified as DAPI-, CD14+. For identifying methylprednisolone effects on activated cells For identifying methylprednisolone effects on activated cells, instead of plasmablasts, lineage- HLA-DRhigh cells were sorted (identified as DAPI-, CD14-, CD19-, CD3-, and HLA-DRhigh). After sorting of the cells using FACS technology, the cells were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (v2, dual index) following the manufacturer’s instructions. Some PBMC were first stimulated with virus-specific peptide-pools for 16 hours in the presence of blocking antibodies for CD28 and CD40. These cells were sorted for expression of DAPI- and dump- (CD14 and CD19) and CD3+, CD154+ and CD69+.
The purified cDNA was amplified and then used for 5’ gene expression (GEX), CITE-Seq and TCR library preparation using the Single Cell 5’ Library & Gel Bead Kit (v2, 10x Genomics). TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human T cells. Through fragmentation, adapter ligation and index PCR the final GEX and TCR libraries were obtained. The CITE-Seq libraries were obtained only by index PCR. The quality of single cell 5’ GEX, CITE-Seq and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq2000 (or NextSeq500) device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 90nt, index1: 10nt, index2: 10nt) and NextSeq 1000/2000 P3 reagent kits.

treatment_protocol: Patients were treated accodring to standard of care. For dataset before and after Methylprednisolone puls children were treated with methylprednisolon 20-30 mg/kg(bodyweight)/day for 3 consecutive days. B07 (MIS-C patient Berlin 07), B09 and B 10 were captured before treatment with methylprednisolone, B08 was treated with 1-2mg/kg methylprednisolone for 2 days, B06 was treated with 1-2 mg/kg methylprednisolone for 3 days. Patients B01, B02 B04, B05 and B11 were treated with 20-30 mg/kg methylprednisolone for 1 day and B03 was treated with 20-30 mg/kg methylprednisolone for 4 days before capturing.


title: sorted cells from 2 patients with influenza

description: Library name: Pool_R4_L5_GEX

source_name: sorted cells from peripheral blood

value: sorted cells from peripheral blood


title: FS-830 [CD4]


title: FS-887

description: CD14 MicroBeads, human (Miltenyi Biotec)

source_name: CD14+ monocytes

extract_protocol: Cells were extracted using CD14 microbeads (Miltenyi Biotec). DNA was prepared using QIAamp DNA Mini Kit (Qiagen)


title: HCC biopsy 2_nonresponse

value: Imperial College London


title: Naïve_1


title: sorted cells from 2 patients with influenza_hashtags

description: Library name: Pool_R4_L5_CITE

library_source: other

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.h5 files containing the information needed to evaluate date in R using Seurat (e.g.)
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files containing the B-cell receptor informations for the samples.
Library strategy: CITE-seq

molecule: other

tag: hto

value: hashtag1, hashtag 3


title: sorted cells from 4 patients with MIS-C_25-28_hashtags

description: Library name: EBV_pool8_CITE

source_name: sorted activated b cells from peripheral blood


title: FS-795


title: FS-877 [CD4]


title: HCC biopsy 1_response


title: sorted cells from 4 patients with MIS-C_13-16_hashtags

description: Library name: EBV_pool5_CITE

value: sorted activated b cells from peripheral blood


title: sorted cells from 1 patient with influenza_#6

description: Library name: Pool_D6I2_GEX


title: sorted cells from 1 patient with influenza_#6_hashtags

description: Library name: Pool_D6I2_CITE


title: sorted T cells from 4 patients including 2 patients with influenza_#1and#3_hashtags

description: Library name: actTcells_all_CITE

value: sorted activated T cells from peripheral blood


title: sorted cells from 4 patients with MIS-C_25-28

description: Library name: EBV_pool8_GEX


title: FS-796


title: sorted cells from 4 patients with MIS-C_21-24_hashtags

description: Library name: EBV_pool7_CITE


title: sorted cells from 4 patients with MIS-C_17-20

description: Library name: EBV_pool6_GEX


title: sorted cells from 4 patients with MIS-C_17-20_hashtags

description: Library name: EBV_pool6_CITE


title: sorted cells from 4 patients with MIS-C_21-24

description: Library name: EBV_pool7_GEX


title: sorted cells from 4 patients with MIS-C_9-12

description: Library name: EBV_pool4_GEX


title: sorted cells from 4 patients with MIS-C_5-8

description: Library name: EBV_pool2_GEX


title: sorted cells from 4 patients with MIS-C_13-16

description: Library name: EBV_pool5_GEX


title: FS-877


title: sorted cells from 4 patients with MIS-C_5-8_hashtags

description: Library name: EBV_pool2_CITE


title: sorted cells from 4 patients with MIS-C_1-4

description: Library name: EBV_pool1_GEX


title: bfCLIP of mESCs: ZFP207 R2

city: Hangzhou, Zhejiang, China

first: yuenan

last: zhou

address: Yuhangtang Road, Hangzhou, Zhejiang, 310058, China

department: School of Medicine

description: RIP-Seq

data_processing:
The analysis of CLIP-seq data was performed using CLIP Tool Kit (CTK, v1.1.3) .
The processed reads were mapped to the mouse genome (Ensembl annotation of mm10) using BWA v0.7.17 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Mouse ESC were cultured in complete ESC medium (DMEM, 15% FCS, 1× pen/strep, with the addition of 0.1 mM non-essential amino acid, 1 mM L-glutamine, 0.1 mM beta-mercaptoethanol, and 1,000 U/ml leukemia inhibitory factor).

extract_protocol:
Pre-equilibrated FLAG magnetic beads (Beyotime) were added to cell lysate, and then the ligated RNAs were further purified using TRIzol reagent.
CLIP-seq libraries constructed followed the eCLIP protocol as descripted in Van Nostrand et al., 2016.

treatment_protocol: ZFP207AID mESCs were cultured in complete ESC medium, with or without the addition of IAA for 5 hours.

tag: cell line

value: embryonic stem cells

value: ZFP207 FLAG-biotin-tagged-2

value: ZFP207 AID0h-2


title: FS-884

value: female


title: sorted cells from 4 patients with MIS-C_9-12_hashtags

description: Library name: EBV_pool4_CITE


title: bfCLIP of mESCs: ZFP207AID+IAA

description: RIP-Seq

value: WT

value: ZFP207 AID5h


title: FS-880


title: sorted cells from 4 patients with MIS-C_1-4 _hashtags

description: Library name: EBV_pool1_CITE


title: bfCLIP of mESCs: negative control

description: RIP-Seq

value: BirA


title: 4sU-seq of mESCs: ZFPAID5h R2

data_processing:
For the analysis of 4sU-seq data, we aligned the 4sU-seq clean reads to the mouse genome assembly mm10 using Hisat2 v2.2.1 with default parameters.
For differential gene expression analysis, gene-level read counts were quantified using StringTie v2.2.1 (the key parameter: --rf) and normalized by variance-stabilizing transformation using DESeq2 v1.42.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Library strategy: 4sU-seq

extract_protocol:
The 4sU labelled RNAs were further biotinylated using biotin-HPDP and enriched by streptavidin beads.
RNA-seq libraries were constructed using RNA-seq Library Prep Kit (Vazyme) following the manufacturer’s instructions.

value: ZFP207 degration

value: AID 5h


title: 4sU-seq of mESCs: ZFPAID5h R3


title: U1 RAP-seq of ZFP207 AID 5h, R2

data_processing:
The processed reads were first aligned to rRNA and U1 snRNA using Bowtie2.2.5 in order to remove them.
The remaining reads were aligned to Dmel6.42 and mm10 with Hisat2.2.1, respectively.
The mapping ratio of drosophila used to correct bedgraph for converting to bigWig.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: RAP-seq

extract_protocol:
The eluent RNAs by U1 probes were further reverse-crosslinked by irradiating with 254 nm UV in the presence of acridine orange for 15 minutes, and then used for subsequent library construction.
Custom strand-specific RNA-Sequencing.

value: ZFP207AID 5h


title: bfCLIP of mESCs: ZFP207 R1

description: RIP-Seq

value: ZFP207 FLAG-biotin-tagged-1

value: ZFP207 AID0h-1


title: 4sU-seq of mESCs: ZFPAID5h R1


title: U1 RAP-seq of ZFP207 AID 5h, R1


title: U1 RAP-seq of ZFP207 AID 0h, R2

value: ZFP207AID 0h


title: 4sU-seq of mESCs: ZFPAID0h R2

value: AID 0h


title: U1 RAP-seq of ZFP207 AID 0h, R1


title: 4sU-seq of mESCs: ZFPAID0h R1


title: 4sU-seq of mESCs: ZFPAID0h R3


title: CRISPRi screen of B2G-U1-PAS mESCs: D8 R2

description: CRISPRi screen

data_processing:
Pooled CRISPR screens were analyzed using the MAGeCK pipeline.
Briefly, raw sequencing reads from next-generation sequencing were trimmed and aligned to the reference using Bowtie v1.3.1 to determine sgRNA counts in each sample.
Counts files for samples subjected to comparison were processed by using MAGeCK MLE.
The beta scores and P-values were calculated using MAGeCK MLE for target genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Library strategy: CRISPR screen

extract_protocol:
Genomic DNAs were extracted and amplified for high-throughput sequencing of sgRNA abundance.
PCR amplification of pooled oligo library.

treatment_protocol: For mESC transfection, 12-24 hours after transfection, the medium was replaced with the appropriate medium containing the respective drugs (hygromycin B, 250 μg/mL, blasticidin, 20 μg/mL) for the selection of stable cell lines.

value: CRISPRi D8

value: CRISPRi screen blasticidin selection 8 days


title: CRISPRi screen of B2G-U1-PAS mESCs: D8 R1

description: CRISPRi screen


title: ZFP207AID mESCs, 4sU label R2

description: For calling T-to-C mismatch ratio

data_processing:
For PAR-bioRIP analysis, we first used bowtie2 v2.2.5 to align the processed reads exclusively to the Rnu1a1 isoform of U1 snRNA with the following key parameters: --sensitive-local --no-unal -k 1.
Subsequently, pysamstats v1.1.2 was utilized with identical aforementioned parameters to identify the T-to-C ratio.
The scatter plot only depicted the base-level T-to-C ratio of the common region from all U1 snRNA isoforms.
Assembly: Rnu1a1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

extract_protocol:
The eluted RNA was extracted, and reverse transcription was performed using a specific primer targeting the 3’ end of U1 snRNA.
The full-length U1 snRNA was then amplified, and a library was constructed for deep sequencing.

treatment_protocol: To identify ZFP207’s binding site on U1 snRNA, we cultured ZFP207AID mESCs in medium containing 200 μM 4sU for 24 hours to do PAR-bioRIP.

value: 4sU label

value: ZFP207AID, 4sU label 24h


title: FS-881

value: male


title: CRISPRi screen of B2G-U1-PAS mESCs: D5 R2

description: CRISPRi screen

value: embryonic stem cells

value: CRISPRi D5

value: CRISPRi screen blasticidin selection 5 days


title: FS-830

value: female


title: ZFP207AID mESCs, Input R2

description: Input as negative control

value: Input

value: Wild type


title: ZFP207AID mESCs, 4sU label R1

description: For calling T-to-C mismatch ratio


title: CRISPRi screen of B2G-U1-PAS mESCs: D5 R1

description: CRISPRi screen


title: ZFP207AID mESCs, Input R1

description: Input as negative control


title: 4sU-seq of ZFP207 AID mESCs rescued by N78 mutation of ZFP207 R1

description: ZFP207AID_N78 R1

treatment_protocol: The truncation/mutation-rescued ZFP207AID mESCs were cultured in complete ESC medium, with the addition of IAA for 5 hours.

value: N78 mutation of ZFP207 R1

value: rescued by N78 mutation of ZFP207 R1


title: 4sU-seq of ZFP207 AID mESCs rescued by ZF1,2-H2A mutation of ZFP207 R1

description: ZFP207AID_ZF1,2-H2A R1

value: ZF1,2-H2A mutation of ZFP207 R1


title: 4sU-seq of ZFP207 AID mESCs rescued by ZF1,2-H2A mutation of ZFP207 R2

description: ZFP207AID_ZF1,2-H2A R2

value: ZF1,2-H2A mutation of ZFP207 R2


title: 4sU-seq of ZFP207 AID mESCs rescued by N78-FUS-IDR mutation of ZFP207 R1

description: ZFP207AID_N78-FUS-IDR R1

value: N78-FUS-IDR mutation of ZFP207 R1


title: CRISPRi screen of B2G-U1-PAS mESCs: D0 R2

description: CRISPRi screen

value: WT

value: CRISPRi screen control, D0


title: 4sU-seq of ZFP207 AID mESCs rescued by N78-FUS-IDR mutation of ZFP207 R2

description: ZFP207AID_N78-FUS-IDR R2

value: N78-FUS-IDR mutation of ZFP207 R2


title: 4sU-seq of ZFP207 AID mESCs rescued by N78 mutation of ZFP207 R2

description: ZFP207AID_N78 R2

value: N78 mutation of ZFP207 R2

value: rescued by N78 mutation of ZFP207 R2


title: 4sU-seq of ZFP207 AID mESCs rescued by N-IDR1 mutation of ZFP207 R2

description: ZFP207AID_N-IDR1 R2

value: N-IDR1 mutation of ZFP207 R2

value: rescued by N-IDR1 mutation of ZFP207 R2


title: 4sU-seq of ZFP207 AID mESCs rescued by empty vector R1

description: ZFP207AID_EV R1

value: embryonic stem cells

value: empty vector R1

value: ZFP207 AID5h R1


title: 4sU-seq of ZFP207 AID mESCs rescued by full-length of ZFP207 R2

description: ZFP207AID_FL R2

value: full-length of ZFP207 R2

value: rescued by full-length of ZFP207 R2


title: TT-seq of mESCs: ZFP207AID5h 4sU 10min

description: TT-seq

data_processing:
For the analysis of TT-seq data, we aligned the TT-seq clean reads to the mouse genome assembly mm10 using Hisat2 v2.2.1 with default parameters.
After obtaining the BAM file, it was converted into a BED12 format using bedtools v2.28, and then split into spliced and unspliced BED files for overlapping with the intron loci of each gene.
To assess the splicing efficiency of each intron, we selected spliced and unspliced reads that spanned the boundary between the last nucleotide of the intron and the initial nucleotide of its adjacent downstream exon for calculation.
These spliced and unspliced counts were then normalized to RPM (reads per million mapped reads), and we compared the fold change between ZFP207AID mESC treated with IAA for 5 hours or untreated control.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: TT-seq

value: ZFP207 degradation

value: AID 5h


title: 4sU-seq of mESCs: SNRNP70AID0h R1

treatment_protocol: SNRNP70AID mESCs were cultured in complete ESC medium, with or without the addition of IAA for 5 hours.

value: AID 0h


title: 4sU-seq of mESCs: SNRNP70AID5h R1

value: SNRNP70 degration


title: 4sU-seq of ZFP207 AID mESCs rescued by N-IDR1 mutation of ZFP207 R1

description: ZFP207AID_N-IDR1 R1

value: N-IDR1 mutation of ZFP207 R1

value: rescued by N-IDR1 mutation of ZFP207 R1


title: 4sU-seq of mESCs: SNRNP70AID0h R2

value: WT


title: 4sU-seq of ZFP207 AID mESCs rescued by full-length of ZFP207 R1

description: ZFP207AID_FL R1

value: full-length of ZFP207 R1

value: rescued by full-length of ZFP207 R1


title: 4sU-seq of mESCs: SNRNP70AID5h R2


title: 4sU-seq of ZFP207 AID mESCs rescued by empty vector R2

description: ZFP207AID_EV R2

value: empty vector R2

value: ZFP207 AID5h R2


title: TT-seq of mESCs: ZFP207AID0h 4sU 10min

description: TT-seq


title: planktonic-rna-1

status: Public on Dec 22 2024

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version _A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 2 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 2 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Assembly: ASM18296v3
Supplementary files format and content: raw counts table

organism: Candida albicans

source_name: fungal cells

growth_protocol: A 25 mL overnight culture of C. albicans strain DK318 (Banerjee, et al., Mol. Biol.Cell 19(4):1354-1365, 2008) was grown in YEPD (yeast extract peptone dextrose) at 30°C. Cells were harvested and washed in sterile DPBS (Dulbecco’s phosphate buffered saline (GIBCO)). The cell pellet was then resuspended and diluted to 1 x 106 cells/mL in pre-warmed RPMI-1640 medium (Sigma-Aldrich). Biofilms were formed in six 150 cm2 canted neck cell culture flasks (Corning) by adding 30 mL of pre-warmed RPMI1640 medium containing 1 x 106 cells/mL.  The flasks were incubated at 37°C for 6 hrs. at 25 RPM. At the end of the incubation, media was carefully aspirated from the flasks and the biofilm was washed three times with ice cold sterile DPBS to remove non-adherent cells. Biofilm cells were then scraped off the flasks and collected by rapid filtration. Next, the pellet was resuspended in lysis buffer (1x yeast polysome buffer (Illumina), 1% Triton X-100, (Sigma), 50 ug/mL GMPPNP (Sigma), 10 ug/mL Blasticidin S (InvivoGen)), snap frozen in liquid nitrogen and stored at -80°C until use.Planktonic cultures were grown by inoculating an equivalent number of cells from the same overnight culture used to initiate biofilm formation in 100 mL of pre-warmed RPMI-1640 medium. The culture was incubated at 37°C for 6 hrs. at 200 RPM. Cells were harvested by rapid filtration and the pellet was washed three times with ice cold sterile DPBS. The planktonic culture cell pellet was suspended in lysis buffer, snap frozen and stored at -80°C as described above.The experiments were performed using 3 independent biological replicates.

extract_protocol:
Cell lysates were prepared as described previously ((Mundodi, et al., G3 11(2):jkaa043 (2021) and Choudhary, et al., Microbiol. Spectr. 11(5):e0257223 (2023)), except that samples were lysed by bead beating 6 times for 1 min. each with a 1 min. rest on ice between vortexes. Cells were recovered by filtration at room temperature, rapidly scraped off the filter paper with a cell scraper, placed into ice-cold lysis buffer (1x yeast polysome buffer (Illumina), 1% Triton X-100, (Sigma), 50 ug/mL GMPPNP (Sigma), 10 ug/mL Blasticidin S (InvivoGen)), and  homogeneously mixed, followed by snap freezing in liquid nitrogen. Cell lysates were prepared and ribosome profiling was performed using three biological replicates as we have described previously (Mundodi, et al., G3 11(2):jkaa043 (2021) and Choudhary, et al., Microbiol. Spectr. 11(5):e0257223 (2023)).
Ribosome profiling and library preparation were carried out according to the protocol described for the True Seq Ribo Profile (Yeast) Kit (Illumina). Lysates were digested with 15 U RNase I (Ambion) per A260 unit and incubated at room temperature for 45 min. with gentle rotation. The reactions were stopped by the addition of 1000U/mL SUPERase-IN (Ambion). 80S monosome fractions were purified from the cell lysate using MicroSpin S-400 HR columns (GE Healthcare). Ribosome protected fragments (RPFs) were further purified using the RNA Clean & Concentrator-25 Kit (Zymo Research) method. This kit was also used for total RNA purification. rRNA depletion was carried out using a Ribo-Zero Magnetic Gold (Yeast) kit (Illumina). An additional subtraction step was included to remove rRNA sequences from circularized cDNA as described previously (Spealman et al. 2016) with slight modifications. Subtractions were carried out in a 30 uL reaction volume, with 10 uL sample, 2 uL 20X SSC and 2 uL of a rRNA subtraction pool containing custom-designed biotinylated oligonucleotides (see Dataset S8 in Mundodi, et al., G3 11(2):jkaa043 (2021)). The circularized DNA was next used as a template for amplification of library PCR products. PCR products of 140-160 bp were recovered from excised gel slices, quantified by Agilent Bioanalyzer/Fragment analyzer and deep sequencing was performed using an Illumina Hiseq3000 machine at the Greehey Children’s Cancer Research Institute Genome Sequencing Facility (University of Texas Health Science Center at San Antonio). All ribosome profiling experiments were performed in biological triplicate.

value: fungal cells

tag: growth condition

value: planktonic


title: planktonic-rna-2

institute: University of Texas Health Science Center at San Antonio


title: planktonic-rna-3


title: Family 4 Genomic DNA

status: Public on Dec 29 2024

city: Pittsburgh

first: Quasar

last: Padiath

state: PA

address: 130 DeSoto St., Dept. of Human Genetics

department: Human Genetics

institute: University of Pittsburgh

hyb_protocol: Samples and hybridization buffer (Agilent Oligo aCHG/ChIP-on-chip Hybridization Kit) were combined and applied to microarrays (Design# 035726_20110728) enclosed in Agilent SureHyb chambers. Hybridization was carried out for 24 hours at 65°C.

scan_protocol: After hybridization, slides were sequentially washed. Sample were then scanned in an G2565CA Agilent microarray scanner at 5 µm resolution.

data_processing: aCGH data was extracted using Agilent’s Feature Extraction program and assessed for quality based on background noise, signal intensity, signal-to-noise ratio, reproducibility, and derivative log ratio standard deviation. Following extraction, the raw data were normalized to the control (Cy3) and analyzed using Agilent Cytogenetics version 4.0.3.12. Human genome assembly GRCh38/hg38 was used for all genome coordinates.

source_name: Blood

label_protocol: DNA test and reference samples (0.2 µg each) were digested with Alu I and Rsa I for 2 hours at 37°C, followed by heat inactivation for 20 minutes at 65°C. After digestion and inactivation, the DNA was labeled using Cy5-dUTP for the test samples and Cy3-dUTP for the reference samples, and then purified using the Agilent SureTag DNA Labeling Kit.

extract_protocol: Genomic DNA from whole blood was isolated using the Gentra Puregene kit (Qiagen) according to the manufacturer’s instructions.

value: Male

tag: clinical phenotype

value: ADLD

tag: tissue

value: Blood

value: Female

tag: clincal phenotype

value: No ADLD

tag: sample type

value: Control


title: CRISPRi screen of B2G-U1-PAS mESCs: D0 R1

description: CRISPRi screen

value: embryonic stem cells

tag: genotype

value: CRISPRi screen control, D0


title: planktonic-ribo-3

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version _A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 2 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 2 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Assembly: ASM18296v3
Supplementary files format and content: raw counts table
Library strategy: Ribo-seq


title: planktonic-ribo-2


title: planktonic-ribo-1


title: biofilm-ribo-3

value: biofilm


title: biofilm-ribo-1


title: SZ_chip_S0456_wapl_s_flag_clone3_with_iaa_rep2

status: Public on Dec 21 2024

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

data_processing:
Conventional ChIP-seq processing pipeline were adopted. Briefly, paired-end reads were aligned to mouse reference genome mm9 through the Bowtie2 (v2.3.5.1) software with default parameters and soft clipping allowed ("--local"). All unmapped reads and low quality alignments with MAPQ score lower than 30 was removed using SAMtools (v1.9). PCR duplicates were removed using Picard (v2.23.3) with default parameters. Reads aligned to mitochondria, random contigs and ENCODE blacklisted regions were also removed using BEDtools (v2.27.1)(2). Counts per million mapped reads (CPM) normalization was performed using the bamCoverage function of Deeptools (v3.1.3).
In-situ Hi-C data from each individual clone or biological replicates were aligned to mouse reference genome mm9 using bowite2 (global parameters: --very-sensitive -L 30 --score-min L, -0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder). Reads were paired up and PCR duplicates were removed through the Hi-C Pro software (v3.0.0) to generate a valid interaction pair file. The output pair files were then converted to “.hic” files using the hicpro2juicebox utility. HiC files were also converted to “.cool” files using the Hicexplorer (v3.7). For replicate or clone-merged samples, similar steps were taken on reads merged from each clone or biological replicates.
Assembly: mm9
Supplementary files format and content: cool, hic and bigwig files of each individual biological replicate are provided.

source_name: erythroid

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultured in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
For Hi-C, FACS purified cells (0.1 million) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water. For ChIP-seq, FACS purified cells were re-suspended in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl and 0.2% NP-40) supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. Notably, for Rad21 ChIP-seq experiments in the WapldTag/SororinmAID and WapldTag/SMC2mAID/SororinmAID cells, roughly 30% of crosslinked 293T cells were added into the cell mixture. Nuclei were then pelleted and re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 20min on ice. Chromatin was then fragmented by sonication (Qsonica Q800R3, 80% amplitude, 20s ON, 40s OFF) for 17min. Cell debris were removed by centrifugation at 15000g for 10min at 4℃. The supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) supplemented with protease inhibitor, PMSF and 50ul of A/G agarose beads (Santa Cruz Cat#sc-2003). Preclear of chromatin was performed at 4℃ for 4-8h with rotation. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with antibody and incubated on a rotator at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200μl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP and input chromatin were reverse crosslinked at 65℃ overnight in the presence of proteinase K. IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with PCR purification kit (QIAGEN Cat#28106).
For Hi-C, DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacturer's protocol. To elute DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform. For ChIP, libraries were constructed using the VAHTS Universal DNA Library Prep Kit for MGI (Vazyme, Cat#NDM607-02) according to the manufacturer's protocol. ChIP libraries were sequenced on the MGI DNBSEQ-T7 sequencing platform.
HiC and ChIP-seq libraries were constructed using the VATHS DNA library preparation kit from Vazyme (N607) according to the manufacturer's protocol.

treatment_protocol: The G1E-ER4 derivative cell lines: Wapl-dTag/SMC2-AID; Wapl-dTag/Sororin-AID (with or without Sororin-9A) and Wapl-dTag/SMC2-AID/Sororin-AID (with or without Sororin-9A mutant) were arrested by RO3306 at G2/M transition with combinations of dTag13 and 5-Ph-IAA treatment. Samples were then released from RO-3306 for either 4h or 30min for mitotic enrichment before FACS purification.

value: erythroid

value: G1E-ER4 cells

value: erythroblasts

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(8h)


title: SZ_chip_S0457_wapl_sororin_flag_clone4_no_iaa

value: RO-3306 arrest (20h) and release (4h); dTag13(8h)


title: SZ_chip_S0458_wapl_sororin_flag_clone4_with_iaa


title: SZ_chip_S0455_wapl_s_flag_clone3_no_iaa_rep2


title: SZ_chip_S0454_wapl_s_flag_clone3_with_iaa_rep1


title: SZ_chip_S0453_wapl_sororin_flag_clone3_no_iaa_rep1


title: SZ_chip_S0452_wapl_sororin_flag_clone2_with_iaa


title: wapl_sororin_with_a_with_d_g2_clone16

description: sororin(-); cohesive-cohesin(-); extrusive-cohesin(excessive)

value: Wapl-dtag/Sororin-aid


title: biofilm-rna-3

value: fungal cells


title: wapl_sororin_with_a_with_d_g2_clone17


title: SZ_chip_S0451_wapl_sororin_flag_clone2_no_iaa


title: wapl_sororin_with_a_no_d_g2_clone17

description: sororin(-); cohesive-cohesin(-)


title: wapl_sororin_asyn_g1_clone17


title: wapl_sororin_asyn_g2_clone16


title: wapl_sororin_with_a_no_d_g2_clone16

description: sororin(-); cohesive-cohesin(-)


title: biofilm-rna-2


title: wapl_sororin_asyn_g2_clone17


title: wapl_sororin_no_a_no_d_g2_clone16

description: sororin(+); cohesive-cohesin(+)


title: biofilm-rna-1


title: wapl_sororin_asyn_g1_clone16


title: biofilm-ribo-2


title: wapl_smc2_with_a_pmpm2_mid_clone1


title: wapl_smc2_with_a_pmpm2_low_clone9


title: wapl_smc2_with_a_pmpm2_mid_clone9


title: wapl_smc2_with_a_pmpm2_high_clone9


title: wapl_smc2_with_a_pmpm2_low_clone1


title: wapl_smc2_with_a_pmpm2_g2_clone1


title: wapl_smc2_no_a_pmpm2_mid_clone1


title: wapl_smc2_no_a_pmpm2_mid_clone9


title: wapl_smc2_no_a_pmpm2_low_clone9


title: wapl_sororin_no_a_with_d_g2_clone16

description: sororin(+); cohesive-cohesin(+); extrusive-cohesin(excessive)


title: wapl_sororin_no_a_no_d_g2_clone17

description: sororin(+); cohesive-cohesin(+)


title: wapl_smc2_no_a_pmpm2_low_clone1


title: wapl_smc2_no_a_pmpm2_high_clone9


title: wapl_sororin_no_a_with_d_g2_clone17


title: wapl_smc2_no_a_pmpm2_high_clone1


title: wapl_smc2_no_a_pmpm2_g2_clone9


title: wapl-smc2_M_with_a_with_d_Rad21_clone1-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)

value: Nocodazole (4h); 5_Ph_IAA(8h); dTag13(8h)


title: wapl-smc2_M_with_a_with_d_input_clone1-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_CTCF_clone9-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_Rad21_clone9-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_Rad21_clone1-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_Rad21_clone9-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_CTCF_clone9-rep0_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_with_a_with_d_CTCF_clone1-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl_smc2_with_a_pmpm2_g2_clone9


title: wapl-smc2_M_no_a_with_d_Rad21_clone1-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)

value: Nocodazole (4h); dTag13(8h)


title: wapl_smc2_with_a_pmpm2_high_clone1


title: wapl-smc2_M_no_a_with_d_Rad21_clone9-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_with_a_with_d_Rad21_clone1-rep3_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_M_no_a_with_d_input_clone1-rep2_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_CTCF_clone1-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_CTCF_clone9-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_Rad21_clone9-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_CTCF_clone9-rep0_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_Rad21_clone1-rep3_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl-smc2_M_no_a_with_d_CTCF_clone1-rep0_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl_smc2_no_a_pmpm2_g2_clone1


title: wapl-smc2_asyn_with_d_Rad21_clone9-rep2_10_percent_293T

description: asyn; Wapl(-)

value: dTag13 (4h)


title: wapl-smc2_asyn_with_d_input_clone1-rep2_10_percent_293T

description: asyn; Wapl(-)


title: wapl-smc2_asyn_no_d_Rad21_clone9-rep0_10_percent_293T

description: asyn; Wapl(+)


title: wapl-smc2_asyn_with_d_CTCF_clone9-rep2_10_percent_293T

description: asyn; Wapl(-)


title: wapl-smc2_asyn_with_d_Rad21_clone1-rep2_10_percent_293T

description: asyn; Wapl(-)


title: wapl-smc2_asyn_with_d_CTCF_clone1-rep2_10_percent_293T

description: asyn; Wapl(-)


title: wapl-smc2_M_with_a_with_d_CTCF_clone1-rep0_10_percent_293T

description: mitosis; Wapl(-); SMC2(-)


title: wapl-smc2_asyn_no_d_Rad21_clone1-rep0_10_percent_293T

description: asyn; Wapl(+)


title: wapl-smc2_asyn_no_d_CTCF_clone9-rep0_10_percent_293T

description: asyn; Wapl(+)


title: wapl-smc2_asyn_no_d_input_clone1-rep0_10_percent_293T

description: asyn; Wapl(+)


title: wapl_smc2_M_no_a_no_d_clone1

description: mitosis; Wapl(+); SMC2(+)

value: Nocodazole (4h)


title: wapl_smc2_asyn_with_d_clone9

description: asyn; Wapl(-)


title: wapl_smc2_M_no_a_with_d_clone1

description: mitosis; Wapl(-); SMC2(+)


title: wapl_smc2_M_no_a_no_d_clone9

description: mitosis; Wapl(+); SMC2(+)


title: wapl-smc2_M_no_a_with_d_Rad21_clone1-rep1_10_percent_293T

description: mitosis; Wapl(-); SMC2(+)


title: wapl_smc2_asyn_with_d_clone1

description: asyn; Wapl(-)


title: wapl-smc2_asyn_no_d_CTCF_clone1-rep0_10_percent_293T

description: asyn; Wapl(+)


title: rad21_configuration8_light_load_clone8_9aa_S0301

description: mitosis: condensin(-);extrusive-cohesin(+);cohesive-cohesin(+)

value: Wapl-dtag/SMC2-aid/Sororin-aid + Sororin-9A mutant

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(4.75h)


title: wapl_smc2_asyn_no_d_clone9

description: asyn; Wapl(+)


title: wapl_smc2_asyn_no_d_clone1

description: asyn; Wapl(+)


title: rad21_configuration8_light_load_clone5_rep3_S0394


title: rad21_configuration8_light_load_clone5_9aa_S0300


title: rad21_configuration8_clone8_9aa_S0288


title: rad21_configuration8_clone5_rep4_S0393


title: rad21_configuration8_clone8_9aa_S0287


title: rad21_configuration7_short_release_clone8_S0418

description: mitosis: condensin(-);extrusive-cohesin(-);cohesive-cohesin(+)

value: RO-3306 short_arrest (8h) and short_release (30min); 5_ph_IAA (8.5h); dTag13(-)


title: rad21_configuration8_clone5_9aa_S0286


title: rad21_configuration7_clone8_S0295

value: RO-3306 arrest (20h) and release (4h); 5_ph_IAA (24h); dTag13(-)


title: rad21_configuration7_short_release_clone7_S0417


title: rad21_configuration6_light_load_clone5_rep4_S0391

description: mitosis: condensin(-);extrusive-cohesin(+);cohesive-cohesin(-)


title: rad21_configuration7_short_release_clone5_S0416


title: rad21_configuration7_clone5_rep3_S0389


title: rad21_configuration7_clone5_rep4_S0390


title: rad21_configuration6_light_load_clone5_rep3_S0388


title: wapl_smc2_M_no_a_with_d_clone9

description: mitosis; Wapl(-); SMC2(+)


title: rad21_configuration6_clone8_S0280


title: rad21_configuration6_clone5_S0279


title: rad21_configuration6_clone5_S0278


title: rad21_configuration6_clone8_S0281


title: rad21_configuration6_clone5_rep3_S0383


title: rad21_configuration4_light_load_clone17_9aa_S0299

description: mitosis: condensin(+);extrusive-cohesin(+);cohesive-cohesin(+)

value: Wapl-dtag/Sororin-aid + Sororin-9A mutant


title: rad21_configuration4_light_load_clone17_9aa_S0298


title: rad21_configuration4_light_load_clone16_9aa_S0297

description: mitosis:condensin(+);extrusive-cohesin(+);cohesive-cohesin(+)


title: rad21_configuration4_light_load_clone16_9aa_S0296


title: rad21_configuration4_clone17_rep3_S0385


title: rad21_configuration4_clone17_9aa_S0285


title: rad21_configuration4_clone16_rep3_S0384


title: rad21_configuration4_clone16_9aa_S0283


title: rad21_configuration4_clone16_9aa_S0282


title: rad21_configuration2_light_load_rep3_S0387

description: mitosis:condensin(+);extrusive-cohesin(+);cohesive-cohesin(-)


title: rad21_configuration2_clone17_S0277


title: rad21_configuration2_light_load_rep3_S0386


title: rad21_configuration2_clone17_rep3_S0382


title: rad21_configuration2_clone16_S0276


title: rad21_configuration7_clone5_S0293


title: rad21_configuration2_clone16_S0275


title: flag_configuration8_light_load_clone7_9aa_S0311

description: mitosis:condensin(-);extrusive-cohesin(+);cohesive-cohesin(+)


title: flag_configuration8_clone8_9aa_S0447


title: flag_configuration8_clone7_9aa_S0435


title: flag_configuration8_clone5_9aa_S0446


title: flag_configuration8_clone5_9aa_S0434


title: flag_configuration8_clone7_9aa_S0310


title: flag_configuration7_short_release_clone8_S0424

description: mitosis:condensin(-);extrusive-cohesin(-);cohesive-cohesin(+)


title: flag_configuration7_short_release_clone7_S0423


title: flag_configuration7_short_release_clone5_S0422


title: flag_configuration7_clone8_9aa_S0309


title: flag_configuration7_clone7_9aa_S0308


title: flag_configuration4_light_load_clone17_9aa_S0306


title: flag_configuration4_light_load_clone16_9aa_S0304


title: flag_configuration4_light_load_clone16_9aa_S0303


title: flag_configuration4_clone17_9aa_S0433


title: flag_configuration4_light_load_clone17_9aa_S0305


title: flag_configuration4_clone17_9aa_S0438


title: flag_configuration4_clone16_9aa_S0432


title: flag_configuration4_clone17_9aa_S0318


title: flag_configuration4_clone17_9aa_S0319


title: flag_configuration4_clone16_9aa_S0316


title: flag_configuration4_clone16_9aa_S0317


title: flag_configuration4_clone16_9aa_S0437


title: rad21_configuration2_clone16_rep3_S0381


title: configuration4_light_load_clone17_9aa


title: configuration4_light_load_clone16_9aa


title: configuration4_clone16_9aa


title: configuration2_light_load_clone17

description: mitosis: condensin(+);extrusive-cohesin(+);cohesive-cohesin(-)


title: configuration2_light_load_clone16


title: configuration2_clone17


title: configuration2_clone16


title: configuration3_clone17_9aa

description: mitosis: condensin(+);extrusive-cohesin(-);cohesive-cohesin(+)


title: configuration3_clone16_9aa


title: configuration3_short_release_clone17


title: configuration1_clone17

description: mitosis: condensin(+);extrusive-cohesin(-);cohesive-cohesin(-)


title: configuration3_short_release_clone16


title: configuration1_clone16


title: configuration1_short_release_clone17


title: configuration1_short_release_clone16


title: configuration9_clone1


title: configuration8_light_load_clone8_9aa


title: configuration8_light_load_clone5_9aa


title: configuration8_clone8_9aa


title: configuration8_clone5_9aa


title: configuration4_clone17_9aa


title: configuration6_light_load_clone7


title: configuration6_clone8


title: configuration6_clone5


title: configuration7_clone5_9aa


title: configuration7_clone7_9aa


title: configuration6_light_load_clone5


title: configuration6_clone7


title: configuration7_clone8_9aa