title: BC003ALMkP27well54

description: single cell RNA


title: BC003ALMkP27well4

status: Public on Nov 07 2021

type: SRA

city: Norwich

first: Edyta

last: Wojtowicz

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: single cell RNA

library_source: transcriptomic

data_processing:
Reads were trimmed (adapters, quality) using Trim_Galore (v 0.5) and mapped to the mouse genome (mm38) using STAR (2.6.0)
Reads mapping unambiguously to exons within genes were counted with HTSeq (0.6.1)
Genome_build: mm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: MkP

extract_protocol:
Bone marrow cells were isolated by crushing, stained with antibodies and FACS-purified on BD FACS Melody, sorted directly into lysis buffer and frozen at-80 before further processing.
standard Smart Seq2 library followed by Nextera protocol from Illumina.
single cell RNA-seq

tag: strain

tag: tissue

value: bone marrow

tag: age

value: 32-weeks post transplantation

tag: genotype

value: WT

tag: treatment

value: control


title: BC003ALMkP27well53

description: single cell RNA


title: BC003ALMkP27well51

description: single cell RNA


title: BC003ALMkP27well52

description: single cell RNA


title: BC003ALMkP27well48

description: single cell RNA


title: BC003ALMkP27well50

description: single cell RNA


title: BC003ALMkP27well46

description: single cell RNA


title: BC003ALMkP27well45

description: single cell RNA


title: BC003ALMkP27well43

description: single cell RNA


title: BC003ALMkP27well44

description: single cell RNA


title: BC003ALMkP27well47

description: single cell RNA


title: BC003ALMkP27well41

description: single cell RNA


title: BC003ALMkP27well5

description: single cell RNA


title: BC003ALMkP27well42

description: single cell RNA


title: BC003ALMkP27well36

description: single cell RNA


title: BC003ALMkP27well58

description: single cell RNA


title: BC003ALMkP27well34

description: single cell RNA


title: BC003ALMkP27well40

description: single cell RNA


title: BC003ALMkP27well38

description: single cell RNA


title: BC003ALMkP27well3

description: single cell RNA


title: BC003ALMkP27well33

description: single cell RNA


title: BC003ALMkP27well2

description: single cell RNA


title: BC003ALMkP27well37

description: single cell RNA


title: BC003ALMkP27well35

description: single cell RNA


title: BC003ALMkP27well32

description: single cell RNA


title: BC003ALMkP27well30

description: single cell RNA


title: BC003ALMkP27well31

description: single cell RNA


title: BC003ALMkP27well49

description: single cell RNA


title: BC003ALMkP27well27

description: single cell RNA


title: BC003ALMkP27well28

description: single cell RNA


title: BC003ALMkP27well26

description: single cell RNA


title: BC003ALMkP27well25

description: single cell RNA


title: BC003ALMkP27well24

description: single cell RNA


title: BC003ALMkP27well23

description: single cell RNA


title: BC003ALMkP27well22

description: single cell RNA


title: BC003ALMkP27well1

description: single cell RNA


title: BC003ALMkP27well29

description: single cell RNA


title: BC003ALMkP27well14

description: single cell RNA


title: BC003ALMkP27well17

description: single cell RNA


title: BC003ALMkP27well10

description: single cell RNA


title: BC003ALMkP27well20

description: single cell RNA


title: BC003ALMkP27well39

description: single cell RNA


title: BC003ALMkP27well21

description: single cell RNA


title: BC003ALMkP27well18

description: single cell RNA


title: BC003ALMkP27well16

description: single cell RNA


title: BC003ALHSC91

description: single cell RNA

source_name: HSC


title: BC003ALHSC89

description: single cell RNA


title: BC003ALHSC8

description: single cell RNA


title: BC003ALMkP27well11

description: single cell RNA


title: BC003ALMkP27well15

description: single cell RNA


title: BC003ALHSC9

description: single cell RNA


title: BC003ALMkP27well13

description: single cell RNA


title: BC003ALHSC96

description: single cell RNA


title: BC003ALHSC94

description: single cell RNA


title: BC003ALMkP27well12

description: single cell RNA


title: BC003ALHSC95

description: single cell RNA


title: BC003ALHSC93

description: single cell RNA


title: BC003ALHSC85

description: single cell RNA


title: BC003ALMkP27well19

description: single cell RNA


title: BC003ALHSC87

description: single cell RNA


title: BC003ALHSC90

description: single cell RNA


title: BC003ALHSC86

description: single cell RNA


title: BC003ALHSC88

description: single cell RNA


title: BC003ALHSC84

description: single cell RNA


title: BC003ALHSC92

description: single cell RNA


title: BC003ALHSC79

description: single cell RNA


title: BC003ALHSC82

description: single cell RNA


title: BC003ALHSC7

description: single cell RNA


title: BC003ALHSC81

description: single cell RNA


title: BC003ALHSC80

description: single cell RNA


title: BC003ALHSC83

description: single cell RNA


title: BC003ALHSC78

description: single cell RNA


title: BC003ALHSC76

description: single cell RNA


title: BC003ALHSC75

description: single cell RNA


title: BC003ALHSC77

description: single cell RNA


title: BC003ALHSC74

description: single cell RNA


title: BC003ALHSC73

description: single cell RNA


title: BC003ALHSC70

description: single cell RNA


title: BC003ALHSC68

description: single cell RNA


title: BC003ALHSC71

description: single cell RNA


title: BC003ALHSC69

description: single cell RNA


title: BC003ALHSC67

description: single cell RNA


title: BC003ALHSC65

description: single cell RNA


title: BC003ALHSC66

description: single cell RNA


title: BC003ALHSC61

description: single cell RNA


title: BC003ALHSC63

description: single cell RNA


title: BC003ALHSC64

description: single cell RNA


title: BC003ALHSC5

description: single cell RNA


title: BC003ALHSC60

description: single cell RNA


title: BC003ALHSC57

description: single cell RNA


title: BC003ALHSC53

description: single cell RNA


title: BC003ALHSC56

description: single cell RNA


title: BC003ALHSC62

description: single cell RNA


title: BC003ALHSC52

description: single cell RNA


title: BC003ALHSC51

description: single cell RNA


title: BC003ALHSC55

description: single cell RNA


title: BC003ALHSC6

description: single cell RNA


title: BC003ALHSC72

description: single cell RNA


title: BC003ALHSC50

description: single cell RNA


title: BC003ALHSC58

description: single cell RNA


title: BC003ALHSC46

description: single cell RNA


title: BC003ALHSC49

description: single cell RNA


title: BC003ALHSC4

description: single cell RNA


title: BC003ALHSC45

description: single cell RNA


title: BC003ALHSC48

description: single cell RNA


title: BC003ALHSC38

description: single cell RNA


title: BC003ALHSC41

description: single cell RNA


title: BC003ALHSC35

description: single cell RNA


title: BC003ALHSC47

description: single cell RNA


title: BC003ALHSC43

description: single cell RNA


title: BC003ALHSC40

description: single cell RNA


title: BC003ALHSC27

description: single cell RNA


title: BC003ALHSC29

description: single cell RNA


title: BC003ALHSC59

description: single cell RNA


title: BC003ALHSC26

description: single cell RNA


title: BC003ALHSC3

description: single cell RNA


title: BC003ALHSC44

description: single cell RNA


title: BC003ALHSC25

description: single cell RNA


title: BC003ALHSC39

description: single cell RNA


title: BC003ALHSC37

description: single cell RNA


title: BC003ALHSC36

description: single cell RNA


title: BC003ALHSC19

description: single cell RNA


title: BC003ALHSC54

description: single cell RNA


title: BC003ALHSC33

description: single cell RNA


title: BC003ALHSC34

description: single cell RNA


title: BC003ALHSC32

description: single cell RNA


title: BC003ALHSC31

description: single cell RNA


title: BC003ALHSC18

description: single cell RNA


title: BC003ALHSC30

description: single cell RNA


title: BC003ALHSC14

description: single cell RNA


title: BC003ALHSC11

description: single cell RNA


title: BC003ALHSC12

description: single cell RNA


title: BC003ALHSC24

description: single cell RNA


title: BC003ALHSC16

description: single cell RNA


title: BC003ALHSC17

description: single cell RNA


title: BC003ALHSC28

description: single cell RNA


title: BC003ALHSC23

description: single cell RNA


title: BC003ALHSC2

description: single cell RNA


title: BC003ALHSC42

description: single cell RNA


title: BC003ALHSC21

description: single cell RNA


title: BC003ALHSC22

description: single cell RNA


title: BC003ALCFU96

description: single cell RNA

source_name: CFU


title: BC003ALHSC20

description: single cell RNA


title: BC003ALCFU94

description: single cell RNA


title: BC003ALCFU91

description: single cell RNA


title: BC003ALCFU90

description: single cell RNA


title: BC003ALCFU89

description: single cell RNA


title: BC003ALHSC1

description: single cell RNA


title: BC003ALHSC10

description: single cell RNA


title: BC003ALHSC13

description: single cell RNA


title: BC003ALHSC15

description: single cell RNA


title: BC003ALCFU95

description: single cell RNA


title: BC003ALCFU81

description: single cell RNA


title: BC003ALCFU83

description: single cell RNA


title: BC003ALCFU93

description: single cell RNA


title: BC003ALCFU80

description: single cell RNA


title: BC003ALCFU92

description: single cell RNA


title: BC003ALCFU8

description: single cell RNA


title: BC003ALCFU88

description: single cell RNA


title: BC003ALCFU86

description: single cell RNA


title: BC003ALCFU85

description: single cell RNA


title: BC003ALCFU87

description: single cell RNA


title: BC003ALCFU71

description: single cell RNA


title: BC003ALCFU84

description: single cell RNA


title: BC003ALCFU7

description: single cell RNA


title: BC003ALCFU79

description: single cell RNA


title: BC003ALCFU64

description: single cell RNA


title: BC003ALCFU62

description: single cell RNA


title: BC003ALCFU9

description: single cell RNA


title: BC003ALCFU78

description: single cell RNA


title: BC003ALCFU61

description: single cell RNA


title: BC003ALCFU77

description: single cell RNA


title: BC003ALCFU60

description: single cell RNA


title: BC003ALCFU82

description: single cell RNA


title: BC003ALCFU67

description: single cell RNA


title: BC003ALCFU73

description: single cell RNA


title: BC003ALCFU74

description: single cell RNA


title: BC003ALCFU5

description: single cell RNA


title: BC003ALCFU55

description: single cell RNA


title: BC003ALCFU57

description: single cell RNA


title: BC003ALCFU58

description: single cell RNA


title: BC003ALCFU69

description: single cell RNA


title: BC003ALCFU54

description: single cell RNA


title: BC003ALCFU6

description: single cell RNA


title: BC003ALCFU72

description: single cell RNA


title: BC003ALCFU70

description: single cell RNA


title: BC003ALCFU53

description: single cell RNA


title: BC003ALCFU68

description: single cell RNA


title: BC003ALCFU66

description: single cell RNA


title: BC003ALCFU65

description: single cell RNA


title: BC003ALCFU51

description: single cell RNA


title: BC003ALCFU4

description: single cell RNA


title: BC003ALCFU63

description: single cell RNA


title: BC003ALCFU44

description: single cell RNA


title: BC003ALCFU59

description: single cell RNA


title: BC003ALCFU43

description: single cell RNA


title: BC003ALCFU42

description: single cell RNA


title: BC003ALCFU41

description: single cell RNA


title: BC003ALCFU56

description: single cell RNA


title: BC003ALCFU49

description: single cell RNA


title: BC003ALCFU40

description: single cell RNA


title: BC003ALCFU48

description: single cell RNA


title: BC003ALCFU50

description: single cell RNA


title: BC003ALCFU39

description: single cell RNA


title: BC003ALCFU46

description: single cell RNA


title: BC003ALCFU47

description: single cell RNA


title: CRISPRi-empty hPGCLC rep3

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

country: China

institute: Zhejiang University

data_processing:
Fastqc v0.11.8 (Andrews, 2010) was used for quality control. No sequence trimming was performed based on quality control.
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97 from Ensembl (Yates et al., 2020). The reads was allowed to map to maximum of 1,000 loci and the best hit was kept (--outFilterMultimapNmax 1000 –outSAMmultNmax 1).
Counts for both gene and transposable elements were calculated (parameter for gene “-p”, parameters for TE “-p -M”) by FeatureCounts v2.0.0 (Liao et al., 2014). Annotation file for genes was from Ensembl (Yates et al., 2020) by using GRCh38.97. Annotation file for transposable elements (TE) was based on repeatmasker (http://repeatmasker.org/) by using GRCh38.
Differentially expressed genes (DEGs) and transposable elements (DETEs) were generated by R package DESeq2 v1.26.0 (Love et al., 2014). The RPKM mean of either control group or treatment group was greater than 1, with 1.5-fold change and 0.05 FDR for DEGs, 4-fold change and 0.05 FDR for DETEs.
Deeptools bamCoverage v3.4.3 (Ramírez et al., 2014) was used to generate bigwig tracks.
Genome_build: hg38
Supplementary_files_format_and_content: txt format, count file for each sample; bigwig format, tracks for each sample

organism: Homo sapiens

source_name: Day 4 hPGCLCs made from UCLA2 hESCs

growth_protocol: UCLA2 hESCs were cultured in hESC media as previously described (Chen et al, 2018). The differentiation of hPGCLCs in vitro was performed as described in (Chen et al., 2017; Sasaki et al., 2015). Day-4 hPGCLC aggregates were collected for further analysis.

extract_protocol:
hPGCLC aggregates were dissociated with 0.05% Trypsin-EDTA for 10 min at 37°C. The dissociated cells were then stained with Integrin α6-Brilliant Violet 421 and EpCAM-AlexaFluor 488 conjugated antibodies, washed with FACS buffer (1% BSA in PBS) and resuspended in FACS buffer (1% BSA in PBS) with 7-AAD (BD PharMingen, 559925) as a viability dye. Cells were sorted using FACS into 350 uL of RLT Buffer (Qiagen). RNA was extracted using RNeasy micro kit (Qiagen).
RNA-seq libraries were constructed by using Ovation Rapid Library Systems (Tecan, 0319-32) and quantified by a KAPA library quantification kit (Kapa Biosystems, kk4824).

treatment_protocol: hESCs were transduced with lentivirus encoding dCas9-KRAB fusion protein and validated gRNAs targeting LTR5Hs (Pontis et al., 2019), or without gRNA as control. After transduction, hESCs were recovered in hESC media supplemented with 10 mM ROCKi and 1ug/ml puromycin. Puromycin selection was used to screen for positive cells for at least 5 days. Following five days of puromycin selection, surviving cells were then into hPGCLCs for both CRISPRi and control lines using normal protocols.

tag: cell type

value: Day 4 hPGCLCs made from UCLA2 hESCs

tag: culture condition

value: hPGCLC media

tag: genotye

value: Empty-gRNA, dCas-KRAB transduction

tag: passage number


title: BC003ALCFU36

description: single cell RNA


title: BC003ALCFU45

description: single cell RNA


title: BC003ALCFU38

description: single cell RNA


title: CRISPRi-LTR5Hs hPGCLC rep3

value: LTR5Hs-gRNA, dCas-KRAB transduction


title: CRISPRi-LTR5Hs hPGCLC rep2


title: SOX17 input hPGCLC rep2

library_source: genomic

data_processing:
Fastqc v0.11.8 (Andrews, 2010) was used for quality control. No sequence trimming was performed based on quality control.
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38. The reads was allowed to map to maximum of 1,000 loci with no more than 3 mismatches, and the best hit was kept (--outFilterMultimapNmax 1000 --outFilterMismatchNmax 3 --outSAMmultNmax 1). Mapping reads over splice junction was not allowed by building STAR index without general feature format file and disallowing intron length (--alignIntronMax 1).
PCR duplicates were removed by Samtools v1.9 (Li et al., 2009) rmdup function.
Deeptools bamCoverage v3.4.3 (Ramírez et al., 2014) was used to generate bigwig tracks.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) by setting ChIP files as treatment and input files as control.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format, peak tracks for each sample

molecule: genomic DNA

growth_protocol: UCLA2 hESCs were cultured in hESC media as previously described (Chen et al, 2018). The differentiation of hPGCLCs in vitro was performed as described in (Chen et al., 2017; Sasaki et al., 2015). Day-4 hPGCLC aggregates of confluent hESCs were collected for further analysis as detailed below.

extract_protocol:
Pellets were thawed on ice and resuspending in lysis buffer at room temperature, rotating for 15 minutes. The resulting lysate was pelleted by 5 minutes of centrifugation at 4000 RPM. Pellet was re-suspended in Nuclei isolation buffer at 4°C, rotating for 10 minutes followed by 5 minutes of centrifugation at 4000 RPM. The resulting pellet was resuspended in 10 mM Tris HCl pH 8, 10 mM EDTA, 0.5 mM EGTA with protease inhibitors. Samples were sonicated and insoluble material was removed. 10% of resulting soluble supernatant was saved as an input sample. To pre-clear, Protein A beads were washed in dilution buffer three times. Protein A beads were resuspended in dilution buffer and added to samples so that Protein A Dynabeads were suspended in a volume of dilution buffer equal to the volume of soluble material. Chromatin was pre-cleared by incubation with Protein A Dynabeads for 2 hours, rotating at 4°C. Beads were removed and anti-SOX17 antibody (AF1924, R and D Systems) or anti-NANOG antibody (AF1997, R and D Systems) were added and allowed to incubate rotating at 4°C overnight. Antibodies were bound for recovery using Protein G Dynabeads by incubation at 4°C, rotating for two hours. Antibody-bound beads were washed and chromatin was eluted from beads by incubating at 65°C, rotating at 1400 RPM in 50mM Tris HCl pH8, 1mM EDTA, 1% SDS two times. To facilitate crosslinking reversal, eluate was left to incubate at 65°C overnight. Eluate was treated with RNase A at 37°C for 30 minutes followed by treatment with Proteinase K at 56°C. DNA was purified using Qiagen PCR purification kit according to manufacturer’s instructions.
ChIP-seq libraries were generated using using Tecan Genomics Ovation UltraLow V2 DNA-seq (0344NB, Redwood City, CA) according to the manufacturer’s instructions. All ChIP-seq libraries were sequenced using a NovaSeq 6000 (Illumina, San Diego) on an NovaSeq SP lane using paired-end 100 base pair reads.

treatment_protocol: hPGCLC aggregates were dissociated with 0.05% Trypsin-EDTA for 10 min at 37°C. The dissociated cells were then stained with Integrin α6-Brilliant Violet 421 and EpCAM-AlexaFluor 488 conjugated antibodies, washed with FACS buffer (1% BSA in PBS) and resuspended in FACS buffer with 7-AAD (BD PharMingen, 559925) as a viability dye. Cells were sorted by FACS into 5% FBS-supplimented hPGCLC media. Following FACS, cell were fixed using 1% formaldehyde, rotating at room temperature for 10 minutes. Fixation was quenched using 0.14M Glycine. Cells were pelleted by centrifugation at 3000 RPM for 5 minutes. Resulting cell pellets were flash frozen in liquid nitrogen and stored at -80°C prior to immunoprecipitation. For hESC samples, confluent hESCs were treated with 0.05% Trypsin for 3 minutes. MEFs were then depleted and the resulting hESCs were fixed and stored as above.

value: wild type

tag: chip antibody


title: BC003ALCFU34

description: single cell RNA


title: BC003ALCFU52

description: single cell RNA


title: BC003ALCFU3

description: single cell RNA


title: CRISPRi-LTR5Hs hPGCLC rep1


title: CRISPRi-empty hPGCLC rep2


title: Enzalutamide_9

city: Toronto

first: Lisanne

last: Mout

address: 101 College st

country: Canada

institute: University Health Network

data_processing:
FASTQC v0.11.5
trimmomatic  v0.36
STAR v2.5.3a
AstraZeneca’s disambiguation algorithm  Python variant, 2013
sambamba Flagstat  v0.6.7
FeatureCounts  v1.5.2
DESeq2 package v1.18.1
Genome_build: hg38
Genome_build: mm10

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: PC346C-DCC-K xenograft

growth_protocol: Twenty-one, six weeks old, NMRI nu/nu male mice (Janvier, Le Genest Saint Isle, France) were subcutaneously inoculated with 5*10E6 PC346C-DCC-K cells. Tumor growth was observed after 2-5 weeks in ~80% of the mice.

extract_protocol:
Tumor tissue was lysed and homogenized in QIAzol (ref #79306, Qiagen, Hilden, Germany) using an Ultra-Turrax T25 (Janke & Kunkel, Staufen, Germany). Total RNA was isolated using the miRNA-easy mini kit (ref # 217004, Qiagen), and RNA quality was measured using the Bioanalyzer RNA 6000 Nano assay (ref #5067, Agilent, Santa Clara, California, USA). All RNA samples had a RIN value ≥7.
Library Prep was performed using the NEBNext Ultra Directional RNA Kit for Illumina according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L).
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After mRNA fragmentation, cDNA synthesis was performed and used for ligation with adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. One sample was re-sequenced due high frequency of multi-mapped reads implicating inadequate depletion of ribosomal RNA.

treatment_protocol: Daily oral administration of Enzalutamide (60/mg/kg) or placebo control (vehicle of 1% w/v carboxymethylcellulosesodium salt, with 0.1% v/v Tween 80). Treatment started when xenograft tumors surpassed a volume of 150 mm3 and lasted 7 days.

tag: condition

value: Prostate cancer

tag: gender

value: male

tag: mouse model

value: NMRI nu/nu


title: Enzalutamide_8


title: BC003ALCFU35

description: single cell RNA


title: CRISPRi-empty hPGCLC rep1


title: SOX17 ChIP hPGCLC rep1

value: SOX17 (R&D Systems, AF1924)


title: BC003ALCFU37

description: single cell RNA


title: SOX17 input hPGCLC rep1


title: BC003ALCFU32

description: single cell RNA


title: Enzalutamide_7


title: Enzalutamide_10


title: BC003ALCFU33

description: single cell RNA


title: Enzalutamide_4


title: BC003ALCFU31

description: single cell RNA


title: Enzalutamide_3


title: SOX17 ChIP hESC rep2

source_name: UCLA2 hESCs

value: UCLA2 hESCs

value: hESC media


title: SOX17 input hESC rep2


title: SOX17 ChIP hPGCLC rep2


title: Enzalutamide_2


title: BC003ALCFU30

description: single cell RNA


title: SOX17 ChIP hESC rep1


title: SOX17 input hESC rep1


title: Placebo_4


title: Enzalutamide_1


title: NANOG ChIP hPGCLC rep2

value: Nanog (R&D Systems, AF1997)


title: BC003ALCFU27

description: single cell RNA


title: KO-IRAKM-Low-2_RNA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed ChIP-seq reads were aligned using bowtie 1.1.2
Aligned ChIP-seq reads that overlapped ENCODE blacklist regions were removed
ChIP-seq reads were extended to 250bp
ChIP-seq samples were normalized to sequencing depth and normalized input was subtracted
ChIP-seq samples were converted to BigWig format
RNA-seq trimmed reads were quantified using Salmon v1.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format
Supplementary_files_format_and_content: Quantified RNA-seq transcripts in text

source_name: Bone-marrow derived monocytes

extract_protocol:
RNA was extracted into a 30-µL volume using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen), following the manufacturer’s instruction. 10,000 cells were used to produce each RNA-seq library, with two replicates for each genotype and experimental condition. The extracted mRNA was then concentrated by ethanol precipitation and resuspended in 4.6 µL of RNase-free water. Next, we used the SMART-seq2 protocol, with minor modifications, to prepare cDNA. 2 µL of oligo-dT primer (100 µM) and 2 µL of dNTP mix (10 mM) were added to 2 ng of mRNA in 4.6 µL of water.  The mRNA solution was denatured at 72 °C for 3 min, then immediately placed on ice. Next, 11.4 µL of reverse transcription mix [1 µL of SuperScript II reverse transcriptase (200 U/µL), 0.5 µL of RNAse inhibitor (40 U/µL), 4 µL of Superscript II first-strand buffer, 1 µL of DTT (100mM), 4 µL of 5 M Betaine, 0.12 µL of 1 M MgCl2, 0.2 µL of TSO (100 M), 0.58 µL of nuclease-free water] was added to the mRNA solution. For the reverse transcription reaction, the solution was incubated at 42 °C for 90 min, followed by 10 cycles of 50 °C for 2 min, 42 °C for 2 min, then inactivation at 70 °C for 15 min. 20 µL of the resulting solution (first-strand mixture) was then mixed with 30 µL of PCR mix [25 µL KAPA HiFi HotStart ReadyMix, 0.5 µL IS PCR primers (10 µM), 0.5 µL Evagreen dye, and 4 µL nuclease-free water] and amplified using the program 98 °C for 1 min, followed by 9-11 cycles of 98 °C 15 s, 67 °C 30 s, 72 °C 6 min. Finally, the cDNA was purified using 50 µL of SPRIselect beads.
RNA-seq libraries were generated with the Nextera XT DNA Library Preparation kit (FC-131-1024, Illumina) and manufacturer’s protocol, using approximately 600 pg of purified cDNA from each sample.

treatment_protocol: Cells were cultured in RPMI complete media (RPMI 1640 with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin) along with M-CSF (10 ng/mL) and either PBS, low-dose LPS (100 pg/mL), or high-dose LPS (1 µg/mL). Fresh LPS was added every two days and the cells were harvested after 5 days.

value: IRAK-M-/-

value: Bone-marrow derived monocytes


title: KO-IRAKM-Low-1_RNA


title: BC003ALCFU2

description: single cell RNA

value: bone marrow

value: 32-weeks post transplantation


title: Enzalutamide_6


title: Placebo_2


title: Placebo_5


title: NANOG ChIP hPGCLC rep1


title: BC003ALCFU29

description: single cell RNA

value: WT

value: control


title: Enzalutamide_5


title: BC003ALCFU28

description: single cell RNA


title: Placebo_3


title: NANOG input hPGCLC rep2

value: Day 4 hPGCLCs made from UCLA2 hESCs

value: hPGCLC media


title: KO-IRAKM-High-2_H3K27ac

extract_protocol:
Samples containing 1M cells were centrifuged at 1600 g for 5 minutes at 4°C. Each sample was washed twice with cold 1 mL PBS and resuspended in 9.375mL of PBS. Then, 0.625 mL of 16% formaldehyde was added and the samples were incubated on a shaker for 5 minutes at room temperature. The samples were then quenched with 0.667 mL of 2M glycine and incubated for 5 minutes at room temperature on a rotator. The cells were then centrifuged at 1600 g for 5 minutes and washed twice with 1 mL cold PBS. The pellet was resuspended in 130 µL of Covaris sonication buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.1% SDS and 1x protease inhibitor cocktail (PIC)) and sonicated with a Covaris S220 sonicator using 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 16 minutes at 4°C. Sonicated samples were centrifuged at 16,100 g for 10 minutes at 4°C before the supernatant containing sheared chromatin was removed to a fresh tube. 2.4 µL of sheared chromatin was then mixed with 46.6 µL of IP buffer (20mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, 1% freshly added PMSF and PIC) to generate a 50µL sample containing chromatin from 20,000 cells for MOWChIP-seq.
Libraries for sequencing were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift-Bio).


title: BC003ALCFU24

description: single cell RNA


title: KO-IRAKM-High_input


title: KO-IRAKM-Low-2_H3K27ac


title: Placebo_1


title: KO-IRAKM-High-1_H3K27ac


title: KO-IRAKM-Low_input


title: BC003ALCFU75

description: single cell RNA


title: NANOG ChIP hESC rep2


title: NANOG input hESC rep2


title: BC003ALCFU23

description: single cell RNA


title: BC003ALCFU22

description: single cell RNA


title: KO-IRAKM-PBS-2_H3K27ac


title: KO-IRAKM-Low-1_H3K27ac


title: BC003ALCFU26

description: single cell RNA


title: KO-IRAKM-PBS-1_H3K27ac


title: KO-TRAM-High_input

value: TRAM-/-


title: 48h_C

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
fastqc/0.11.7
trinity, v.2.5.1, --trimmomatic --quality_trimming_params TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25  --SS_lib_type RF
transdecoder/5.0.1/TransDecoder.LongOrfs, "peptide length = 80"
blastp -db uniprot datanase 2018-02-08 --max_target_seqs 1 - evalue 1e-5
hmmscan, database pfam version 31
transdecoder/5.0.1/TransDecoder.Predict --retain_pfam_hits  --retain_blastp_hits
trinity/2.5.1/util/align_and_estimate_abundance.pl --est_method kallisto  --trinity_mode --prep_reference
Genome_build: De novo transcriptome
Supplementary_files_format_and_content: tsv, kallisto read count

organism: Verticillium longisporum

source_name: Mycelia

growth_protocol: Mycelia were grown on PDB for seven days

extract_protocol:
Total RNA was extracted using the RNeasy plant mini kit from Qiagen according to manufacturer's instructions
Sequencing library preparation using TruSeq stranded mRNA library preparation kit with polyA selection (Illumina Inc.)

treatment_protocol: One week after growth on PDB mycelia were treated with 0.05% β-pinene and RNA extracted in different time points

tag: dpi

value: Mycelia


title: KO-TRAM-Low_input


title: KO-IRAKM-PBS_input


title: BC003ALCFU25

description: single cell RNA


title: KO-TRAM-PBS_input


title: NANOG input hESC rep1

value: wild type


title: NANOG input hPGCLC rep1


title: BC003ALCFU20

description: single cell RNA


title: BC003ALCFU21

description: single cell RNA


title: KO-TRAM-High-1_H3K27ac


title: BC003ALCFU1

description: single cell RNA


title: 48h_B


title: KO-TRAM-Low-2_H3K27ac


title: 48h_A


title: NANOG ChIP hESC rep1


title: KO-TRAM-PBS-2_H3K27ac


title: BC003ALCFU19

description: single cell RNA


title: KO-TRAM-PBS-1_H3K27ac


title: 24h_C


title: 7-8-TFAM-KO-2

city: ROCHESTER

first: Xiaochen

last: Gao

state: MN

address: 200 first street SW

department: Immunology

institute: Mayo Clinic

data_processing:
Paired-end libraries were sequenced on an Illumina HiSeq 4000 following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. Base-calling was performed using Illumina’s RTA software (version 2.5.2). Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie (v2.3.4). Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
Differential expression for each gene between various groups was identified by Cuffdiff. For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark and C5 databases of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10
Supplementary_files_format_and_content: csv file include FPKM values for each Sample ...

source_name: Bronchoalveolar lavage

extract_protocol:
Total RNA from in vitro cultured AMs was extracted using RNeasy Plus Mini Kit, and RNA quality was determined (RIN>7) via Agilent Bioanalyzer
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

value: 7-8 weeks

value: TFAM-deficient

value: lung

value: Alveolar macrophages


title: BC003ALCFU18

description: single cell RNA


title: 7-8-TFAM-WT-2


title: 24h_B


title: 7-8-TFAM-KO-1


title: BC003ALCFU17

description: single cell RNA


title: 24h_A


title: 7-8-TFAM-WT-1


title: BC003ALCFU16

description: single cell RNA


title: 3-4-TFAM-KO-2

value: 3-4 weeks


title: KO-TRAM-High-2_H3K27ac


title: 3-4-TFAM-KO-1


title: 3-4-TFAM-WT-2


title: 8h_C


title: 3-4-TFAM-WT-1


title: Ad-Gfp rep3

city: Hangzhou

first: Xiangyu

last: Zhang

address: Xiasha Rd

department: General Surgery Center

institute: Sir Run-Run Shaw Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: abundance measurements

source_name: aorta

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libriaries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HASMCs were treated with Rbm10-associate adenovirus particles overnight and then cultured for 24 hours

value: aorta

tag: agent


title: BC003ALCFU15

description: single cell RNA


title: 8h_B


title: Ad-Gfp rep2


title: KO-TRAM-Low-1_H3K27ac


title: 8h_A


title: BC003ALCFU14

description: single cell RNA


title: BC003ALCFU13

description: single cell RNA


title: BC003ALCFU12

description: single cell RNA


title: Ad-Gfp rep1


title: BC003ALCFU76

description: single cell RNA


title: KODSS_1

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Genome_build: mm10
Supplementary_files_format_and_content: txt files of normalized gene counts for each sample

source_name: Colon

extract_protocol:
Distal colon were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 weeks


title: BC003ALCFU11

description: single cell RNA


title: Ad-Rbm10 rep3

value: Rbm10 adenovirus


title: Ad-Rbm10 rep2


title: WTDSS_1


title: KODSS_2


title: BC003ALCFU10

description: single cell RNA

value: bone marrow


title: Ad-Rbm10 rep1


title: 0h_B


title: 488

status: Public on Nov 06 2021

city: Spokane

first: John

middle: D.

last: Clarke

state: Washington

address: 412 E. Spokane Falls Blvd., 412 E. Spokane Fall BLVD

department: Pharmaceutical Sciences

institute: Washington State University

data_processing:
Initial adapter trimming and fastq formatting was completed with bcl2fastq (v2.17.1.14)
Further adapter trimming and removal of invariant 100th base position of sequencing reads was completed with Trimmomatic (v.0.38) in single-end mode with parameters -phred33 ILLUMINACLIP:TruSeq_i7adapt_SE-MCLR.fa:2:30:10 CROP:99 and a custom adapter file with longer matches to the Illumina adapter sequences used, after which files were concatenated together by sample.
Sequencing reads were aligned to the rat genome (Rnor6.0; Ensembl release 98) using STAR (v. 2.7.3a) with parameters --outMultimapperOrder Random --outSAMtype BAM
Read counts were obtained with featureCounts (Subread 2.0.0) with parameters -s 2 -t exon -g gene_id
Differential gene expression was calculated with DESeq2 (Bioconductor v. 3.10) with "treatment" as a variable (combined dose, diet, post-exposure recovery time) using the Wald test, normal log fold-change (LFC) shrinkage, an LFC threshold of 0.585 (1.5-fold change), and the Benjamini-Hochberg multiple test correction.
Genome_build: Rnor 6.0; Ensembl release 98
Supplementary_files_format_and_content: trim99_recovery.fCounts is a csv file with 1 row per gene of the Ensembl rat build and columns describing:
Supplementary_files_format_and_content: 1) the genes, including the Ensembl Gene Identifier (Geneid), chromosome (Chr), start base position(Start), end base position (End), Strand, and gene length (Length), and
Supplementary_files_format_and_content: 2) 1 column per sample in the study where cell values correspond to the raw counts calculated by featureCounts for each gene for that sample.
Supplementary_files_format_and_content: DGE_tWsN_results is a csv file with 1 row per gene of the Ensembl rat build and column describing:
Supplementary_files_format_and_content: 1) the genes, including the Ensembl Gene Identifier (Geneid), entrezgene identifier (entrezgene_id), accession names (entrezgene_accession), description of the genes,
Supplementary_files_format_and_content: 2) log fold change (LFC) of gene expression comparing HFHC vehicle group versus Control vehicle group after 0 weeks (Column E), 2 weeks (Column M) and 4 weeks (Column U) of recovery and their associated p-adjusted values (Columns F, N and V respectively),
Supplementary_files_format_and_content: 3) log fold change (LFC) of gene expression comparing Control MCLR group versus Control vehicle group after 0 weeks (Column G), 2 weeks (Column O) and 4 weeks (Column W) of recovery and their associated p-adjusted values (Columns H,P and X respectively),
Supplementary_files_format_and_content: 4) log fold change (LFC) of gene expression comparing HFHC MCLR group versus HFHC vehicle group after 0 weeks (Column I), 2 weeks (Column Q) and 4 weeks (Column Y) of recovery and their associated p-adjusted values (Columns J, R and Z respectively),
Supplementary_files_format_and_content: 5) log fold change (LFC) of gene expression comparing HFHC MCLR group versus Control MCLR group after 0 weeks (Column K), 2 weeks (Column S) and 4 weeks (Column AA) of recovery and their associated p-adjusted values (Columns L, T and AB respectively).
Supplementary_files_format_and_content: DGE_tWsN-VST-ctrl_veh_median_normalized is a csv file describing:
Supplementary_files_format_and_content: Row 1(wks_recovery): Number of weeks after recovery from MCLR exposure (0, 2 or 4)
Supplementary_files_format_and_content: Row 2(diet): The diet each animal received, Control (ctrl) or High fat high cholesterol (HFHC)
Supplementary_files_format_and_content: Row 3(dose): The type of dose treatment received by each animal, Vehicle (veh) or MCLR
Supplementary_files_format_and_content: Row 4 (animal): The number designated to each rat in the study
Supplementary_files_format_and_content: Row 5 and below The Ensembl Gene Identifier of each genes (Column A), followed by the normalized median reads of the gene expression.

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Eight-week old male Sprague Dawley rats (n=72) were purchased from Envigo and were maintained in 12 hour light and dark cycles.   Handling, care, and maintenance of the animals was done in the Association for the Assessment of Laboratory Animal Care International accredited program of the Laboratory Animal Resources facility of Washington State University (WSU), Spokane.   All aspects of the animal research were approved by the Institutional Animal Care and Use Committee at Washington State University (approval code 04937).

extract_protocol:
Livers were removed and flash frozen. RNA was extracted with TRIzol reagent from frozen liver tissue according to the manufacturers instructions
mRNA libraries were generated from 1.5 µg using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following standard procedures.

treatment_protocol: Animals were divided into two groups (n=36 per diet group) and fed (ad-libitum) either a control diet or HFHC diet for 8 weeks. Following 8 week diet period, animals were administered vehicle or MCLR via intraperitoneal injections every 48 hours for 2 weeks. Animals were euthanized at three recovery time points: 24 hours (0 week recovery), 2 weeks (2 week recovery) and 4 weeks (4 week recovery) (n=6 per diet and treatment group) after the last MCLR administration.

value: Sprague Dawley

tag: Sex

value: Male

tag: diet

value: HFHC diet  [Rodent diet with 60 kcal% Fat, 10 g Cholesterol and 4g NaCholate; Catalog #D06061401; Research Diets]

value: Microcystin-LR (MCLR)  [30 µg/kg; Catalog #10007188; Cayman Chemicals]

tag: dose volume

value: 5 mL/kg

tag: time

value: 4 week recovery after MCLR


title: 496

tag: strain


title: 494

value: Vehicle[0.9% saline, 0.09% ethanol]


title: 480


title: 495


title: 487


title: 478


title: 0h_A

tag: tissue

value: Mycelia


title: 479

tag: treatment


title: 486


title: 0h_C


title: 492

value: Control diet  [Choline Deficient and Sufficient Iron Supplemented L-AA;   Catlog #518754; Dyets Inc.]


title: 404


title: 484


title: WTDSS_2

tag: age

tag: genotype

value: wild type


title: 485


title: 493


title: 477


title: 481


title: 491


title: 483


title: 403


title: 473


title: 463

value: 2 week recovery after MCLR


title: 490


title: 482


title: 489


title: 462


title: 470


title: 474


title: 454


title: 472


title: 464


title: 469


title: 453


title: 455


title: 459


title: 451


title: 456


title: 452


title: 468


title: 467


title: 458


title: 460


title: 471


title: 466


title: 465


title: 450


title: 461


title: 440

value: 0 week recovery after MCLR


title: 448


title: 439


title: 447


title: 446


title: 431


title: 432


title: 437


title: 443


title: 429


title: 445


title: 430


title: 435


title: 444


title: 438


title: 427


title: 428


title: 441


title: 457


title: 442


title: 449


title: 433


title: 426


title: 425


title: 434


title: 436


title: Healthy-5

city: Hong Kong

first: Pengchao

last: Zhao

address: G10A, RRSSB

department: Biomedical Engineering

institute: Chinese University of Hong Kong

description:
processed data file:
CleanData_stat
ConnectTags_stat
Alpha_diversity
Family.absolute_abundance

data_processing:
library strategy: 16S rDNA
The raw data will be pre-processed to get clean data by in-house procedure as following:
1) Truncation of sequence reads not having an average quality of 20 over a 25 bp sliding window based on the phred algorithm, and trimmed reads having less than 75% of their original length, as well as its paired read, will be removed;
2) Removal of reads contaminated by adapter(default parameter: 15 bases overlapped by reads and adapter with maximal 3 bases mismatch allowed);
3) Removal of reads with ambiguous basa(N base), and its paired reads;
4) Removal of reads with low complexity(default: reads with 10 consecutive same base).
If the two paired-end reads overlapped, the consensus sequence was generated by FLASH (Fast Length Adjustment of Short reads, v1.2.11), and the detailed method is as follows:
1) Minimal overlapping length: 15 bp;
2) Mismatching ratio of overlapped region: <= 0.1.
The tags were clustered to OTU(Operational Taxonomic Unit) by scripts of software USEARCH(v7.0.1090), detailed as follows:
1) The tags were clustered into OTU with a 97% threshold by using UPARSE, and the OTU unique representative sequences were obtained;
2) Chimeras were filtered out by using UCHIME(v4.2.40); The 16S rDNA and ITS sequences were screened for chimeras by mapping to gold database(v20110519）, UNITE(v20140703) separately.
3) All tags were mapped to each OTU representative sequences using USEARCH GLOBAL, then the tags number of each OTU in each sample will be summarized to OTU abundance table.
Databases used for species annotation:
16S rDNA is used for bacterial and archaea community: Greengene(default): V201305[8] ; RDP: Release9 201203[6]
Supplementary_files_format_and_content: Statistics of clean data, tags, alpha diversities, and abundance at family level

organism: rat gut metagenome

source_name: Feces

extract_protocol:
DNA was extracted by BGI Genomics Co., Ltd (Hong Kong). For genomics DNA, we use fusion primer with dual index and adapters for PCR, fragments too short would be removed by Ampure beads.
Standard Illumina protocols

treatment_protocol: The fresh fecal samples in autoclaved sterile vials were properly packaged with dry ice cooling agents and shipped to BGI Genomics Co., Ltd (Hong Kong) for microbiota analyses

value: SD rat

tag: diagnosis

value: healthy

value: Feces

value: Healthy


title: Healthy-3

description: Colon

data_processing:
Library strategy: 16S rDNA
The raw data will be pre-processed to get clean data by in-house procedure as following:
1) Truncation of sequence reads not having an average quality of 20 over a 25 bp sliding window based on the phred algorithm, and trimmed reads having less than 75% of their original length, as well as its paired read, will be removed;
2) Removal of reads contaminated by adapter (default parameter: 15 bases overlapped by reads and adapter with maximal 3 bases mismatch allowed);
3) Removal of reads with ambiguous base (N base), and its paired reads;
4) Removal of reads with low complexity (default: reads with 10 consecutive same base).
If the two paired-end reads overlapped, the consensus sequence was generated by FLASH (Fast Length Adjustment of Short reads, v1.2.11), and the detailed method is as follows:
1) Minimal overlapping length: 15 bp;
2) Mismatching ratio of overlapped region: <= 0.1.
The tags were clustered to OUT (Operational Taxonomic Unit) by scripts of software USEARCH (v7.0.1090), detailed as follows:
1) The tags were clustered into OTU with a 97% threshold by using UPARSE, and the OTU unique representative sequences were obtained;
2) Chimeras were filtered out by using UCHIME (v4.2.40); The 16S rDNA and ITS sequences were screened for chimeras by mapping to gold database (v20110519), UNITE (v20140703) separately.
3) All tags were mapped to each OTU representative sequences using USEARCH GLOBAL, then the tags number of each OTU in each sample will be summarized to OTU abundance table.
Databases used for species annotation:
16S rDNA is used for bacterial and archaea community: Greengene(default): V201305[8] ; RDP: Release9 201203[6].
Supplementary_files_format_and_content: Statistics of clean data, tags, alpha diversities, and abundance at family level.
Supplementary_files_format_and_content: CleanData_stat.txt: Raw counts.
Supplementary_files_format_and_content: ConnectTags_stat.txt: Raw counts.
Supplementary_files_format_and_content: Alpha_diversity.txt: Alpha_diversity.
Supplementary_files_format_and_content: Family.absolute_abundance.txt: Abundance measurements.

extract_protocol:
DNA was extracted by BGI Genomics Co., Ltd (Hong Kong). For genomics DNA, we use fusion primer with dual index and adapters for PCR, fragments too short would be removed by Ampure beads.
Standard Illumina protocols.

treatment_protocol: The fresh fecal samples in autoclaved sterile vials were properly packaged with dry ice cooling agents and shipped to BGI Genomics Co., Ltd (Hong Kong) for microbiota analyses.

tag: rat strain

value: SD


title: Dex-P/PBS-5

value: Colitic

value: Dex-P/PBS


title: Healthy-4


title: Control-5

value: Control


title: Control-4


title: Dex-P/NPA-4

value: Dex-P/NPA


title: Dex-P/PBS-4


title: Healthy-2

description: Colon


title: Healthy-1

description: Colon


title: Dex-P/NPA2-3

description: Colon


title: MDA-MB 468 mock rep3

type: RNA

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

country: Italy

institute: University of brescia

description: replicate 3

hyb_protocol: Following terminal labeling, ss-cDNAs were hybridized in AccuBlockTM Digital Dry Bath for 20 hr at 48°C on HuGene-2_1-st-V1. Array strips were washed and stained in the Affymetrix GeneAtlasTM Fluidic Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlasTM Imaging Station.

data_processing: The data were analyzed with Partek® Genomics Suite® software.

label: biotin

source_name: cells infected with a mock pLentiPGK-Puro (Addgene Plasmid #19070) lentiviral vector

label_protocol: Following fragmentation, biotinylated ss-cDNAs were prepared according to the standard ThermoFisher Scientific protocol from 5.5 ug of ss-cDNA (GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays, ThermoFisher Scientific).

growth_protocol: Cells were grown in DMEM plus 10% FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell line

value: MDA-MB 468

tag: cell type

value: Triple negative breast cancer cells


title: MDA-MB 468 PTX3 rep3

description: replicate 3

source_name: cells infected with a pLentiPGK-Puro (Addgene Plasmid #19070) lentiviral vector harbouring the full length human PTX3 cDNA (GenBank accession n° X63613)


title: MDA-MB 468 PTX3 rep1

description: replicate 1

value: cells infected with a pLentiPGK-Puro (Addgene Plasmid #19070) lentiviral vector harbouring the full length human PTX3 cDNA (GenBank accession n° X63613)


title: MDA-MB 468 mock rep2

description: replicate 2

value: cells infected with a mock pLentiPGK-Puro (Addgene Plasmid #19070) lentiviral vector


title: MDA-MB 468 PTX3 rep2

description: replicate 2


title: MDA-MB 468 mock rep1

description: replicate 1


title: MDA-MB 231 shPTX3 rep2

description: replicate 2

source_name: cells infected with lentiviral vector containing short-hairpin RNA (shRNA) targeting human PTX3 (TRCN0000436981)

value: MDA-MB 231


title: MDA-MB 231 shPTX3 rep1

description: replicate 1

value: cells infected with lentiviral vector containing short-hairpin RNA (shRNA) targeting human PTX3 (TRCN0000436981)


title: MDA-MB 231 shPTX3 rep3

description: replicate 3


title: Dex-P/NPA2-2

description: Colon


title: Dex-P/PBS-3

description: Colon


title: MDA-MB 231 shNT rep1

description: replicate 1

source_name: cells infected with lentiviral vector containing a non-targeting/control sequence (SHC002V, Merck)


title: Mutant CTCF construct R567W rep2

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

data_processing:
Library strategy: Spec-seq
Preliminary processing for each sample: Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
Data quality check between replicates: Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
Specificity and methylation sensitivity analysis: The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Supplementary_files_format_and_content: For each sample, the associated csv file (.processed) contains the bound and unbound reads, calculated relative bindng energy, library type, and epigenetic modifications for individual binding site.

organism: synthetic construct

source_name: Spec-seq sample to synthetic DNA libraries

extract_protocol:
Recombinant protein expression protocol: We used the NEB PURExpress system to produce N-terminal HALO tagged CTCF constructs and noticed better success rates than previous SUMO-tagged constructs.
EMSA protocol: 20uL binding reactions were loaded onto 10% Tris-glycine gel in cold room and run for 50mins at 200V.
Sequencing sample prep protocol: The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer (soaking a 55C for more than 30mins). Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles (annealing temperature 52C, extension time 30s). All samples were pooled together for Illumina Nextseq (1X 75bp single end run).

tag: recombinant protein

value: Mutant CTCF construct (R567W)


title: Mutant CTCF construct R567W rep1


title: Dex-P/NPA-5


title: Dex-P/NPA2-1

description: Colon


title: Wildtype CTCF construct (F1-F11) rep2

value: Wildtype CTCF construct


title: MDA-MB 231 shNT rep2

description: replicate 2

value: cells infected with lentiviral vector containing a non-targeting/control sequence (SHC002V, Merck)


title: Control-2

description: Colon

value: Untreated


title: Dex-P/PBS-1

description: Colon

value: Feces


title: Wildtype CTCF construct (F1-F11) rep1


title: Truncated CTCF construct (F1-F9) rep2

value: Truncated CTCF construct (F1-F9)


title: Truncated CTCF construct (F1-F9) rep1


title: Dex-P/PBS-2

description: Colon

value: SD


title: K562_4BKO-3

city: Miami

first: Karoline

last: Briegel

state: FL

address: 1600 NW 10th Ave

department: Surgery

institute: University of Miami

description: processed data file: K562_comparison_genes.summary.xlsx

data_processing:
After sequencing, the analysis was performed using the in-house developed RNAv9 pipeline which uses a variety of internally developed and open source programs. Many of the tools used were developed at EA | Q² Solutions and are available on the Google code website https://github.com/ExpressionAnalysis/ea-utils/
Any read that has one particular base at ≥ 95% frequency (homopolymer filtering), or has more than 4 Ns within its sequence, or has an average Q score below 25, or has sequence corresponding to a Illumina adapters, or are shorter than 25 nt in length, was removed.
Samples were aligned to the human genome using STAR software version 2.4 and quantified using RSEM version 1.2.14
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gcounts_matrix.annot.xlsx (Excel file) contains counts for each sample.
Supplementary_files_format_and_content: K562_comparison_genes.summary.xlsx (Excel file) contains multiple matrices that summarize the data based on gene counts across all of samples.
Supplementary_files_format_and_content: Field_Descriptions.xlsx (Excel file) contains descriptions of column headers in the K562_comparison_genes.summary.xlsx file.

source_name: K565, ARID4B knockout-3

growth_protocol: K562 cells were grown in RPMI 1640 medium containing 10% FBS, and supplemented with penicillin (100 units/ml) and streptomycin (100 µg/ml).

extract_protocol:
Total RNA was purified using an RNeasy plus kit (Qiagen), and was treated by DNase I (Qiagen).
Samples were prepared and sequenced according to EA | Q² Solutions standard TS Stranded mRNA sequencing protocol using HiSeq - 2x50bp-PE sequencing on an Illumina sequencing platform. RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103), and with dUTP utilized in place of dTTP in the second strand master mix. Forked barcode adaptors were attached to the cDNAs via ligation. The resulting molecules were PCR amplified. Since only the second strand included the dUTP base, stalling the polymerase, the only viable template was the first strand, thereby preserving the strand information. Final libraries are quantified, normalized and pooled for sequencing.

treatment_protocol: K562 cells were incubated at 37°C in 5% CO2 and grown to 50% confluence.

value: Erythroleukemic cell line

tag: genotype/variation

value: ARID4B knockout


title: Control-3

description: Colon

value: Colitic


title: MDA-MB 231 shNT rep3

description: replicate 3


title: K562_4BKO-2

source_name: K565, ARID4B knockout-2


title: K562_4BKO-1

source_name: K565, ARID4B knockout-1


title: Control-1

description: Colon


title: K562_WT-1

source_name: K562, wildtype-1

value: Wildtype


title: K562_WT-3

source_name: K562, wildtype-3


title: L835_drug

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

data_processing:
Avadis NGS Version 2.1 software was used for analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Avadis NGS Version 2.1.
Genome_build: hg19
Supplementary_files_format_and_content: fold-change

source_name: chondrosarcoma

growth_protocol: RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: JJ012 cells were treated with DS-1001b for 1 week and L835 cells were treated for 6 weeks.

value: bone

value: chondrosarcoma

value: 6 weeks after DS-1001b treatment


title: JJ012_control

value: control


title: L835_control


title: K562_WT-2

source_name: K562, wildtype-2


title: Human colon cancer cells - clone E4_no_ab_ChIP_rep3

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

institute: Karolinska Institutet

data_processing:
Basecalls performed using CASAVA version 1.8.2
Chip-seq data was performed by nf-core/chipseq pipeline (version 1.2.2)
Picard (v2.23.1) was used to mark duplicates. BEDTools (v2.29.2) and bedGraphToBigWig were used create normalized bigWig files.
MACS2 (v2.2.7.1) was used to call peaks with following parameter "callpeak --broad --broad-cutoff 0.1-f BAMPE  -g 2.7e9 "
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: Human colon cancer cells

growth_protocol: Human colon cancer cells (HCT-116) were maintained in McCoy's 5A medium modified medium (Life Technologies, 16600-082) supplemented with 10% FBS, and 1% penicillin and streptomycin (Life Technologies)

extract_protocol:
Cells were fixed with 1% freshly prepared formaldehyde solution for 10min and then lysed with buffer containing: 50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS; x1 Proteinase inhibitor (Roche). Chromatin was sonicated and DNA–protein complexes were immune-purified with antibodies against CTCF (CS 2899S)
DNA sample was used for library by following the manufacturer’s recommendations of NEBNext® Ultra™ IIDNA Library Prep Kit (New England BioLabs, US). Index codes were added to each sample. Briefly, the genomic DNA was randomly fragmented to size of 350bp. DNA fragments were end polished, A-tailed, ligated with adapters, size selected and further PCR enriched. Then PCR products were purified (AMPure XP system), followed by size distribution by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), and quantification using real-time PCR. Library was then sequenced on NovaSeq 6000 S4 flow cell with PE150 strategy.

treatment_protocol: No treatment has been involved

tag: chip antibody


title: DHT_1

city: Cambridge

first: Madeline

middle: A

last: Lancaster

state: Cambridgeshire

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
[Bulk RNA-seq]
FASTQ sequence read files were aligned to the hg38 transcriptome (with decoy sequences) and quantified using salmon v0.14.1 applying both a sequence bias correction and a GC bias correction with a mean fragment length of 300 bp and a standard deviation of 50 bp.
Salmon quantification files containing Transcripts Per Million (TPM) estimates were imported into R using tximport v1.16.1 and DESeq2 v1.28.
Prior to analysis, a non-parametric empirical Bayesian batch-correction was applied to the data using the function ‘ComBat’ in sva v3.36.0.
[Single-cell RNA-seq]
Raw sequencing output was converted to the standard fastq format by bcl2fastq, before running through CellRanger Count (version 3.1.0, 10X Genomics) which also performed read alignment using STAR with GRCh38 human reference genome.
The filtered feature barcode matrix for each sample was then analysed further with the Seurat v3 R package by first merging the matrices, followed by removal of cells with mitochondrial percentage >10%, and removal of likely doublets based on nCount_RNA, resulting in a total dataset of 6,899 cells.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: For bulk RNA-seq: Matrix file output (.txt file) from DESeq2.
Supplementary_files_format_and_content: For single-cell RNA-seq: Expression matrix (.txt file) for RNA assay of the processed Seurat object.

source_name: Cerebral organoids

growth_protocol: Organoids were generated from female (XX) H9 human embryonic stem cells. We used the commercial kit (STEMdiff™ Cerebral Organoid Kit, StemCell Technologies 08570) with previously described modifications to increase embryoid body surface area, namely microscaffolds (18000 cells seeded) or smaller EBs (2000 cells seeded). Organoids were transferred to the orbital shaker at 57 rpm (f25 cm) at 15d (±1 day, depending on the morphology). Matrigel® was removed manually between days 14-17, after visual inspection. Organoids were transferred to IDM+A supplemented with diluted Matrigel® on day 30 and kept at those conditions until RNA isolation at Day 35.

extract_protocol:
For bulk RNA-seq, total RNA from individual organoids was isolated using the RNeasy Mini Kit (Qiagen, 74104). Genomic DNA was removed using the Invitrogen TURBO DNA-free kit (Invitrogen, AM1907). After isolation, total RNA from individual organoids of the same treatment was pooled for each library preparation.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) with starting input of 500ng of total RNA per sample. Ribosomal RNA was removed and mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, E7490). During library preparation, AMPure XP Beads (Beckman Coulter, A63881) were used for reaction clean ups. NEBNext Multiplex Oligos (dual index primers) (New England BioLabs, E7600) were used in the PCR enrichment step, with 11 cycles. Library quality was assessed by Bioanalyzer and the concentration was determined using the NEBNext Library Quant Kit for Illumina (New England BioLabs, E7630). Libraries were pooled and sequenced on the HiSeq4000 machine (Illumina) at 50 base pair length, single ended, to a minimum of 30 million reads per library.
For single cell RNA-seq, samples were collected and incubated in 1ml of Accumax (Sigma, A7089) with 400 μg DNase I and 15 μM actinomycin D at 37°C for 20 min with gentle agitation. At 5 min intervals, the sample tubes were flicked, and after 15 min pipetted 10 times, followed by a final pipetting 10 times at 20 min. Clumps were allowed to settle and supernatant collected, to which 100 μl media was added to inactivate Accumax. Samples were then spun at 300xg for 5min. Dead Cell Removal kit and MACS column (Miltenyi, 130-090-101) were used to remove dead cells before another spin at 300g for 5min. Cells were resuspended in an appropriate volume of 0.04% BSA in PBS and loaded on the 10X Chromium system (10X Genomics).
Library preparation was performed using the 10X chromium and single cell RNA-seq libraries were prepared according to manufacturer’s instructions using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) workflow. The Chromium Controller was run according to the protocol producing the single cell gel beads in emulsion mixture. Reverse transcriptase reaction and subsequent amplification were carried out on a C1000 Touch Thermal Cycler (Biorad) and libraries were quality tested using a 2100 Bioanalyzer Instrument (Agilent). Samples were pooled together and sequenced on one lane of SP flowcell of the Novaseq sequencer (Illumina).

treatment_protocol: Media was supplemented with DHT (30 nM), estradiol (100 nM), testosterone (100 nM), or equal volume of ethanol mock control from days 17 to 35.

value: Cerebral organoids

value: DHT

tag: rna isolation

value: 10X single cell

tag: batch/replicate


title: JJ012_drug

value: 1 week after DS-1001b treatment


title: E_1

value: Estradiol


title: E_2


title: DHT_2


title: Control_1

value: Control


title: TNF+TGF-β-Tnfr2-/-#3

city: Bethesda

first: Jonathan

middle: D

last: Ashwell

state: MD

address: Room 3002, Bldg. 37, 9000 Rockville Pike

department: Laboratory of Immune Cell Development

institute: NIH

data_processing:
Adapter trimming: Trimmomatic
Read alignment: STAR v2.5.4 - 2 pass mode
Count normalization: RSEM v1.3.1
Genome_build: mm10
Supplementary_files_format_and_content: RSEM counts

source_name: Splenic CD4+ T cells

growth_protocol: Naïve CD4+ T cells from WT or Tnfr2-/- mice were isolated from spleen and stimulated with anti-CD3/CD28 for 3 days in the presence of the different combinations of cytokines (WT: TNF+TGF-β, Tnfr2-/-: TNF+TGF-β; WT: IL-6+TGF-β) followed by bulk RNA sequence. Each experimental condition was done triplicates and analyzed.

extract_protocol:
Total RNA was isolated from in vitro cultured CD4+ T cells using Qiagen Rneasy mini plus kit.
Clonetech SMARTer Ultra Low Input RNA (v4) for cDNA conversion and Illumina Nextera XT DNA Library Preparation Kit for sequence library prep

treatment_protocol: 24 well cell culture plates were coated with 2 μg/ml of each with anti-CD3 and anti-CD28 antibody, washed with PBS. 5x10^5 naïve CD4+ T cells were stimulated in the presence of 20 ng/ml of IL-6 or TNF and 2 ng/ml of TGF-β.

value: Splenic naive CD4+ T Cells

value: TNF+TGFb


title: Human colon cancer cells - clone E4_no_ab_ChIP_rep2


title: Human colon cancer cells - clone E4_no_ab_ChIP_rep1


title: Control_2


title: Human colon cancer cells - clone D3_no_ab_ChIP_rep3


title: Human colon cancer cells - clone D3_no_ab_ChIP_rep1


title: TNF+TGF-β-Tnfr2-/-#2


title: TNF+TGF-β-Tnfr2-/-#1


title: Human colon cancer cells - clone D3_no_ab_ChIP_rep2


title: TNF+TGF-β-WT#3

value: WT


title: Human colon cancer cells - WT_no_ab_ChIP_rep3


title: Human colon cancer cells - WT_no_ab_ChIP_rep2


title: TNF+TGF-β-WT#1


title: TNF+TGF-β-WT#2


title: Human colon cancer cells - WT_no_ab_ChIP_rep1


title: IL-6+TGF-β-WT#3


title: IL-6+TGF-β-WT#2


title: IL-6+TGF-β-WT#1


title: Human colon cancer cells - clone E4_CTCF_ChIP_rep2

value: CTCF


title: Human colon cancer cells - clone E4_CTCF_ChIP_rep1


title: Human colon cancer cells - clone D3_CTCF_ChIP_rep3


title: WT-Th0#2


title: Human colon cancer cells - WT_CTCF_ChIP_rep3


title: WT-Th0#1


title: Human colon cancer cells - clone D3_CTCF_ChIP_rep2


title: Human colon cancer cells - WT_CTCF_ChIP_rep2


title: Human colon cancer cells - WT_CTCF_ChIP_rep1


title: Human colon cancer cells - clone D3_CTCF_ChIP_rep1


title: EN2dxA: Taenia solium egg, biological rep. 2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description: Taenia solium egg transcriptome

data_processing:
Standard BGISEQ software was used for basecalling
Adaptor-trimmed sequences were quality-checked using FastQC v0.11.5, then mapped (paired-end 100 bp sequences) to the Taenia solium genome (PRJNA170813) and mtDNA (MW718881) using STAR v2.7.5a with the following settings: --outSAMstrandField intronMotif --runThreadN 40 --outFilterIntronMotifs RemoveNoncanonical --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --seedSearchStartLmax 25 --outFilterMatchNmin 0 --alignSoftClipAtReferenceEnds Yes  --outSAMattrIHstart 0  --alignEndsType Local --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMattributes All --outSAMprimaryFlag AllBestScore
FPKM values were calculated using the StringTie v2.1.5 Software with the settings -u -p 40 -e. Single *.gtf files were merged into a list using the StringTie --merge option. StringTie was then run again with the -B option on this merged.gtf list and to produce the final list (*.gene_abund.ballgown.tab) of FPKM values
FPKM and MAP files were generated with StringTie -B (ballgown option) and represent the relative abundance of transcripts/genes
processed data files format and content: EN2dxA_MW718881.cov => base pair exact coverage of Taenia solium mtDNA positions generated with BWA as a space delimited text file
processed data files format and content: EN2dxA.gene_abund.ballgown.tab =>  FPKM and MAP values for all annotated transcripts generated with StringTie -B (ballgown option) as tab delimited text file

organism: Taenia solium

source_name: Taenia solium eggs collected from stool sample

growth_protocol: Taenia solium eggs were collected from fresh stool samples. Tania solium proglottids were obtained by treating patients with niclosamide who were tested positive for tapeworm eggs in stool. Tapeworm proglottids were separated from the worm and washed thoroughly several times in order to remove adherent stool material.

extract_protocol:
Two cleaned Taenia solium eggs were taken up into a total volume of 4 μL of PBS on a fresh cover slide and mounted to a Leica DMiL phase contrast microscope with a HI Plan 20x lens. Two freshly prepared borosilicate needles were inserted into the drop and located under visual control next to the Taenia egg. The two needles were then moved towards each other squeezing and ultimately disrupting the egg. This procedure was repeated for the second egg. The cell lysate was immediately transferred into a 0.5 mL tube containing 0.6 μL of the optimized SMART-Seq buffer, placed on dry ice and shipped on dry ice by an international courier service to the NGS-sequencing facility (BGI, Shenzhen, Guangdong, China)
RNA libraries were prepared for sequencing using standard protocols for BGISEQ-500 sequencing

value: single egg

tag: developmental stage

value: egg

value: unteated, native from stool

tag: origin

value: Zambia


title: RNA-Seq Human colon cancer cells - clone E4 CTCF_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq data was performed by nf-core/rnaseq pipeline (version 3.0)
In brief, adapters and low quality reads were filtered by trimgalore  (0.6.6)[https://github.com/FelixKrueger/TrimGalore]. Clean reads were aligned to the human  reference genome and ERCC RNA spike-in fasta (https://www.thermofisher.com/se/en/home.html)  with hisat2(2.2.0)
Genome-wide coverage output in BEDGRAPH format were generated by Bedtools  genomecov subcommand
UCSC bedSort and bedGraphToBigWig (V377) were used to  Create bigWig coverage files
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Cells were fixed with 1% freshly prepared formaldehyde solution for 10min and then lysed with buffer containing: 50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS; x1 Proteinase inhibitor (Roche). Chromatin was sonicated and DNA–protein complexes were immune-purified with antibodies against CTCF (CS 2899S)
RNA-seq library construction was performed with standard Illumina TruSeq Stranded mRNA kit with  Poly-A selection and samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.0/RTA  v3.4.4) with a 51nt(Read1)-10nt(Index1)-10nt(Index2)-51nt(Read2) setup using 'NovaSeqStandard'  workflow in 'SP' mode flowcell.


title: RNA-Seq Human colon cancer cells - clone D3 CTCF_rep2


title: EN1dxA: Taenia solium egg, biological rep. 1

description: Taenia solium egg transcriptome

data_processing:
Standard BGISEQ software was used for basecalling
Adaptor-trimmed sequences were quality-checked using FastQC v0.11.5, then mapped (paired-end 100 bp sequences) to the Taenia solium genome (PRJNA170813) and mtDNA (MW718881) using STAR v2.7.5a with the following settings: --outSAMstrandField intronMotif --runThreadN 40 --outFilterIntronMotifs RemoveNoncanonical --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --seedSearchStartLmax 25 --outFilterMatchNmin 0 --alignSoftClipAtReferenceEnds Yes  --outSAMattrIHstart 0  --alignEndsType Local --outReadsUnmapped Fastx --outMultimapperOrder Random --outSAMattributes All --outSAMprimaryFlag AllBestScore
FPKM values were calculated using the StringTie v2.1.5 Software with the settings -u -p 40 -e. Single *.gtf files were merged into a list using the StringTie --merge option. StringTie was then run again with the -B option on this merged.gtf list and to produce the final list (*.gene_abund.ballgown.tab) of FPKM values
FPKM and MAP files were generated with StringTie -B (ballgown option) and represent the relative abundance of transcripts/genes
processed data files format and content: EN1dxA_MW718881.cov => base pair exact coverage of Taenia solium mtDNA positions generated with BWA as a space delimited text file
processed data files format and content: EN1dxA.gene_abund.ballgown.tab => FPKM and MAP values for all annotated transcripts generated with StringTie -B (ballgown option) as tab delimited text file

value: untreated, native from stool


title: RNA-Seq Human colon cancer cells - WT CTCF_rep1


title: PROG1: Taenia solium proglottid

description: Taenia solium whole genome and mtDNA sequencing

data_processing:
Library strategy: WGS
Standard Illumina software was used for basecalling
Adaptor-trimmed sequences were quality-checked using FastQC v0.11.5, then mapped as single end reads using BWA MEM v0.7.12 to the contigs representing the Taenia solium genome (NCBI BioProject PRJNA170813) and against Taenia solium mtDNA (GenBank AB086256.1) to generate a BAM file. The mitochondrial sequence of the here investigated worm was further refined using a local realignment with Alfred v0.2.3. This sequence was the placed in GenBank under the accession number MW718881.
The base pair exact coverage of the mtDNA (GenBank MW718881) was calculated using the genomecov module of bedtools v2.23.0
genome build (DNA): Tsolium_Mexico_v1 WBPS15 2014-05-WormBase PRJNA170813
genome build (mtDNA): Genbank MW718881
processed data files format and content: PROG1_MW718881.bam depicts the reads aligned from the PROG1 dataset to the Taenia solium mtDNA
processed data files format and content: PROG1_MW718881.cov => base pair exact coverage of Taenia solium mtDNA positions as a space delimited text file

source_name: Taenia solium worm excreted after niclosamide treatment

extract_protocol:
Whole genomic DNA was isolated from egg containing Taenia solium proglottids after mechanical disruption with a Potter-Elvehjem tissue homogenizer, followed by Proteinase K digest and DNA-cleanup using the Qiagen Powersoil Pro Kit on a QiaCube Connect device according to the manufacturer’s protocol (Qiagen, Hilden, Germany)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Escherichia coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: whole proglottid

value: adult

value: after niclosamide treatment of the patient


title: RNA-Seq Human colon cancer cells - clone E4 CTCF_rep1


title: WT-Th0#3


title: RNA-Seq Human colon cancer cells - clone D3 CTCF_rep1


title: leukocytes - spleen - uninfected

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

description:
SP_CTRL
scRNA-Seq
mRNA

data_processing:
We built a customized genome annotation with full-length cDNA evidence. The modified genome annotation is available at https://github.com/EIB202/Turbot-scRNA and used for building reference with cellranger mkref.
Raw reads were processed with cellranger count. The resulting bam files were used for data submission and the obtained matrices were utilized for cell type identification with Seurat.
Bam files can be converted to fastqs with cellranger bamtofastq.
Genome_build: Turbot_genome.fa.gz; Turbot ensembl v98
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts for every gene.

organism: Scophthalmus maximus

source_name: spleen

growth_protocol: Turbots were reared in a recirculating tank system with seawater for 1 week at 17°C. Edwardsiella piscicida EIB202 was cultivated in Tryptic Soy Broth medium at 30°C.

extract_protocol:
Leukocytes were enriched with percoll discontinuous density gradient centrifugation. mRNA was extracted according to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204 Rev B).
RNA-libraries were prepared according to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204 Rev B).

treatment_protocol: Turbots were incubated in seawater with 2 × 10^7 CFU/mL E. piscicida for 10 min and reared in a clean tank waiting for subsequent sampling.

value: spleen

value: leukocytes

value: untreated

tag: sampling time

value: uninfected


title: leukocytes - spleen - 7 days after infection

description:
SP_7d
scRNA-Seq
mRNA

value: infected with E. piscicida

value: 7 days after infection


title: Human colon cancer cells - clone E4_CTCF_ChIP_rep3


title: Drug3

city: Changchun

first: hui

last: li

address: qianjinstreet

institute: jilin university

data_processing:
Complete the full-length transcriptome sequencing of 6 samples, and the clean data of each sample sequenced reached 4.47GB.
The full length sequence is identified by the primer sequences at both ends of the reads. The number of full length sequences obtained from each sample ranges from 2,635,296 to 4,602,702. Polish the full length sequence to obtain a consensus isoform sequence (consensus isoform). ), all consistent transcript sequences were compared to the reference genome by the software minimap2, and then de-redundancy analysis was performed. Finally, 31,520 transcript sequences were obtained.
Perform fusion transcript prediction on the obtained consistent transcripts. The fusion transcripts obtained for each sample range from 19 to 33. SSR prediction was performed on the transcripts after de-redundancy of all samples, and a total of 44,092 SSRs were obtained. The de-redundant transcripts of all samples were compared and analyzed with the known annotations of the reference genome. There were 1,984 new gene loci and 10,830 newly discovered transcripts. The sequence structure analysis of the newly discovered transcripts was performed. The project predicted a total of 4,761 complete ORF sequences and 158 lncRNAs, and completed the functional annotation of 9,675 new transcripts. Transcription factor prediction was performed on all transcripts, and a total of 1,816 transcription factors were predicted (non-animals and plants cannot be predicted for transcription factors).
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: All_gene_counts.list
Supplementary_files_format_and_content: All_gene_expression.list

source_name: cells

extract_protocol:
The cells are digested and the RNA is harvested using Trizol reagent.
1ug total RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-PCS109) protocol provided by Oxford Nanopore Technologies(ONT).

tag: disease

value: Breast cancer

tag: agent


title: Drug2


title: Drug1


title: Con3


title: leukocytes - spleen - 3 days after infection

description:
SP_3d
scRNA-Seq
mRNA

tag: tissue

tag: treatment

value: 3 days after infection


title: leukocytes - spleen - 21 days after infection

description:
SP_21d
scRNA-Seq
mRNA

value: 21 days after infection


title: Con2


title: Con1


title: leukocytes - spleen - 14 days after infection

description:
SP_14d
scRNA-Seq
mRNA

value: 14 days after infection


title: leukocytes - posterior intestine - uninfected

description:
PI_CTRL
scRNA-Seq
mRNA

source_name: posterior intestine

value: posterior intestine


title: leukocytes - spleen - 12 h after infection

description:
SP_0.5d
scRNA-Seq
mRNA

value: 12 h after infection


title: R_L428-EV-TF-2_SUPHD1-EV-IP-2

city: Groningen

first: Lotteke

last: Ziel-Swier

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Bi9ology

country: Netherlands

institute: UMCG

description:
mRNA and lncRNA expression analysis
AGO2-IP RNA

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: SUPHD1 cell line with empty vector

growth_protocol: L428: RPMI-1640 medium supplemented with 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine and 10 % Fetal Calf Serum; SUPHD1: McCoys5A medium supplemented with 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine and 20 % Fetal Calf Serum;  37⁰C, 5 % CO2.

extract_protocol: miRNeasy Micro/Mini Kit (Qiagen)

treatment_protocol: Cells were transduced with empty lentiviral CD550A-1 vector or lentiviral CD550A-1 miR-150 overexpression construct. GFP+ cells were sorted and subjected to immunoprecipitation using AGO2 ab (Clone 2E12-1C9).

value: SUPHD1 Hodgkin lymphoma cell line

tag: treatment protocol

value: Cells were transduced with empty lentiviral CD550A-1 vector, GFP+ cells were sorted and subjected to immunoprecipitation using AGO2 ab (Clone 2E12-1C9)


title: STICR_Plasmid_Library

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

data_processing:
library strategy: DNA-seq
Fastq files were analyzed using a custom script that used BBDUK to  1) removes low QC reads and 2) retains reads containing known sequence
Using Bowtie, passing reads were then 3) aligned them to a reference list of synthetic sequences
Using awk, extract UMI sequence for each read and output a tab-delimited file of matches sequence and UMI
Using UMI-tools, reduce Sequence-UMI pairs with UMIs within a hamming distance of 1 and export a tab-delimited file containing Sequence and UMI-reduced abundance.
Genome_build: Synthetic reference used
Supplementary_files_format_and_content: TSV format. Contains STICR barcode sequence and UMI-reduced read abundance.

organism: Synthetic plasmid

source_name: Synthetic Plasmid Library

extract_protocol:
Plasmids isolated from ThermoFisher MegaX DH10B bacteria using Macherey-Nagel Gigaprep kit.
Plasmids were digested with XhoI and then ligated to a dsDNA adapter containing a UMI. PCR was then perofrmed to amplify these ligation products and  add Illumina sequencing adapters.

tag: sample type

value: Synthetic Plasmid Library


title: R_L428-miR150-TF-2_SUPHD1-miR150-IP-2

source_name: SUPDH1 cell line with miR-150 overexpression vector

label_protocol: According to the manufacturers instructions

value: Cells were transduced with lentiviral CD550A-1 miR-150 overexpression construct, GFP+ cells were sorted and subjected to immunoprecipitation using AGO2 ab (Clone 2E12-1C9)


title: R_L428-EV-IP-1_SUPHD1-EV-TF-1

description:
mRNA and lncRNA expression analysis
total RNA

value: Cells were transduced with empty lentiviral CD550A-1 vector and GFP+ cells were sorted


title: leukocytes - posterior intestine - 7 days after infection

description:
PI_7d
scRNA-Seq
mRNA


title: STICR_Lentiviral_Library

data_processing:
Fastq files were analyzed using a custom script that used BBDUK to  1) removes low QC reads and 2) retains reads containing known sequence
Using Bowtie, passing reads were then 3) aligned them to a reference list of synthetic sequences
Using awk, extract UMI sequence for each read and output a tab-delimited file of matches sequence and UMI
Using UMI-tools, reduce Sequence-UMI pairs with UMIs within a hamming distance of 1 and export a tab-delimited file containing Sequence and UMI-reduced abundance.
Genome_build: Synthetic reference used
Supplementary_files_format_and_content: TSV format. Contains STICR barcode sequence and UMI-reduced read abundance.

source_name: Lentivirus produced from Synthetic Plasmid Library

extract_protocol:
Unconcentrated lentiviral-laden media was filtered using a 0.45micron filter and then concentrated by ultracentrifugation. Viral pellet was resuspended in 100ul sterile PBS. 5ul of concentrated lentivurs was added to Trizol and RNA was exctracted
RNA was reverse transcribed using a primer targeting the lentiviral transcript, but not anti-sense transcript, to made cDNA. Individual cDNA molecules were tagged with a UMI using a primer during second-strand synthesis. PCR was then perofrmed to amplify these products and  add Illumina sequencing adapters.

tag: molecule subtype

value: Viral RNA


title: R_L428-miR150-IP-1_SUPHD1-miR150-TF-1

tag: cell line

value: Cells were transduced with lentiviral CD550A-1 miR-150 overexpression construct and GFP+ cells were sorted


title: R_L428-miR150-IP-2_SUPHD1-miR150-TF-2


title: R_L428-EV-IP-2_SUPHD1-EV-TF-2


title: leukocytes - posterior intestine - 3 days after infection

description:
PI_3d
scRNA-Seq
mRNA

tag: cell type

value: leukocytes


title: R_L428-miR150-TF-1_SUPHD1-miR150-IP-1


title: leukocytes - posterior intestine - 21 days after infection

description:
PI_21d
scRNA-Seq
mRNA


title: G_L428-EV-TF-2_SUPHD1-EV-IP-2

source_name: L428 cell line with empty vector

value: L428 Hodgkin lymphoma cell line


title: leukocytes - posterior intestine - 14 days after infection

description:
PI_14d
scRNA-Seq
mRNA

value: infected with E. piscicida


title: T 0802

description:
H9_0802_35d_T
salmon-TPM-day35-all-samples.csv

value: Cerebral organoids

value: Testosterone

value: Bulk


title: R_L428-EV-TF-1_SUPHD1-EV-IP-1


title: G_L428-EV-IP-2_SUPHD1-EV-TF-2


title: leukocytes - posterior intestine - 12 h after infection

description:
PI_0.5d
scRNA-Seq
mRNA


title: G_L428-miR150-TF-2_SUPHD1-miR150-IP-2

source_name: L428 cell line with miR-150 overexpression vector


title: leukocytes - head kidney - uninfected

description:
HK_CTRL
scRNA-Seq
mRNA

source_name: head kidney

value: head kidney

value: untreated

value: uninfected


title: G_L428-miR150-IP-2_SUPHD1-miR150-TF-2


title: leukocytes - head kidney - 7 days after infection

description:
HK_7d
scRNA-Seq
mRNA

value: 7 days after infection


title: G_L428-miR150-IP-1_SUPHD1-miR150-TF-1


title: Control 0802

description:
H9_0802_35d_ctrl
salmon-TPM-day35-all-samples.csv

value: Control


title: DHT 0802

description:
H9_0802_35d_DHT
salmon-TPM-day35-all-samples.csv

value: DHT


title: G_L428-miR150-TF-1_SUPHD1-miR150-IP-1


title: G_L428-EV-IP-1_SUPHD1-EV-TF-1

value: Cells were transduced with empty lentiviral CD550A-1 vector, GFP+ cells were sorted and subjected to immunoprecipitation using AGO2 ab (Clone 2E12-1C9)


title: E 1805

description:
H9_1805_35d_E
salmon-TPM-day35-all-samples.csv

value: Estradiol


title: DHT 1805

description:
H9_1805_35d_DHT
salmon-TPM-day35-all-samples.csv


title: G_L428-EV-TF-1_SUPHD1-EV-IP-1

value: Cells were transduced with empty lentiviral CD550A-1 vector and GFP+ cells were sorted


title: leukocytes - head kidney - 21 days after infection

description:
HK_21d
scRNA-Seq
mRNA

value: 21 days after infection


title: T 1805

description:
H9_1805_35d_T
salmon-TPM-day35-all-samples.csv


title: leukocytes - head kidney - 14 days after infection

description:
HK_14d
scRNA-Seq
mRNA

value: 14 days after infection


title: leukocytes - head kidney - 12 h after infection

description:
HK_0.5d
scRNA-Seq
mRNA

value: leukocytes

value: 12 h after infection


title: UN-TUDCA-13

city: Hamamatsu city

first: Misako

last: SUZUKI

state: Shizuoka, Japan

address: Higashi-ku 1-20-1 Handayama

country: Japan

institute: Hamamatsu University School of Medicine.

description: Gene expression data from adipose tisssue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChipTM Hybridization Oven 645(Thermo Fisher Scientific,Inc.). GeneChips were washed and stained in the GeneChipTM Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000 7G(Thermo Fisher Scientific, Inc.)

data_processing: The data were analyzed with Transcriptome Analysis Console(TAC)software version 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: mouse adipose tissue of group UN-RG-TU

label_protocol: Fragmented and Labeled cRNA were prepared according to the GeneChipTM WT PLUS Reagent Kit User Manual(Thermo Fisher Scientific,Inc.)

growth_protocol: Pregnant C57Bl/6 mice were divided into two groups(NN: fed ad libitum with regular chow, UN:restricted to 60% of the energies). In UN dams, the number of pups was adjysted to 4 per litter for the purpose of inducing rapid infantile growth(RG) during lactation period. After weaning, HFD was supplied to all pups from 9 to 17 wks.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: TUDCA  or Vehicle was orally administered between 11 and 16.5 wks.

value: adipose tissue

tag: maternal diet

value: restricted to 60% of the energies

value: TUDCA

tag: strain

tag: Sex

value: male


title: Control 1805

description:
H9_1805_35d_ctrl
salmon-TPM-day35-all-samples.csv

value: Cerebral organoids

tag: rna isolation

value: Bulk


title: UN-TUDCA-14


title: leukocytes - head kidney - 3 days after infection

description:
HK_3d
scRNA-Seq
mRNA

value: head kidney

value: infected with E. piscicida

value: 3 days after infection


title: UN-TUDCA-15


title: UN-Veh-10

source_name: mouse adipose tissue of group UN-Veh

value: vehicle


title: UN-Veh-09


title: UN-TUDCA-16


title: leukocytes - gill - 7 days after infection

description:
GILL_7d
scRNA-Seq
mRNA

source_name: gill

value: gill

value: 7 days after infection


title: E 1706

description:
H9_1706_35d_E
salmon-TPM-day35-all-samples.csv

source_name: Cerebral organoids

value: Estradiol

tag: batch/replicate


title: UN-Veh-12


title: NN-TUDCA-08

source_name: mouse adipose tissue of group NN-RG-TU

value: fed ad libitum with regular chow


title: NN-TUDCA-07


title: UN-Veh-11


title: NN-TUDCA-06


title: DHT 1706

description:
H9_1706_35d_DHT
salmon-TPM-day35-all-samples.csv

value: DHT


title: leukocytes - gill - 3 days after infection

description:
GILL_3d
scRNA-Seq
mRNA

value: leukocytes


title: leukocytes - gill - 21 days after infection

description:
GILL_21d
scRNA-Seq
mRNA

value: 21 days after infection


title: NN-Veh-04

source_name: mouse adipose tissue of group NN-Veh

value: adipose tissue


title: leukocytes - gill - 14 days after infection

description:
GILL_14d
scRNA-Seq
mRNA

value: 14 days after infection


title: leukocytes - gill - 12 h after infection

description:
GILL_0.5d
scRNA-Seq
mRNA

value: 12 h after infection


title: leukocytes - gill - uninfected

description:
GILL_CTRL
scRNA-Seq
mRNA

value: untreated

value: uninfected


title: T 1706

description:
H9_1706_35d_T
salmon-TPM-day35-all-samples.csv

value: Cerebral organoids

value: Testosterone

value: Bulk


title: Myotubes - Control_for _Clenbuterol

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

country: France

institute: Cochin institut

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Fragment per Kilobase of transcript per Million mapped reads (FPKM) and TPM (Transcripts Per Kilobase Million) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: raw counts

source_name: Myotubes - Control_for _Clenbuterol

growth_protocol: DMEM, +2% horse serum, 1% PS

extract_protocol:
Media were removed, and after 1 wash by PBS, RNA was harvested using ISOGEN reagent. Illumina TruSeq stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard TruSeq Stranded mRNA Reference Guide Document # 1000000040498 v00.

treatment_protocol: 30 ng/ml clenbuterol

value: C2C12  myotubes


title: Myotubes - Control_for _EPS

source_name: Myotubes - Control_for _EPS


title: Myotubes - Clenbuterol

source_name: Myotubes - Clenbuterol

tag: group

value: Clenbuterol


title: Myotubes - EPS

source_name: Myotubes - EPS

value: EPS


title: K562 ARID4B ChIP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied.
Sequences (75 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 00DBGWU_K562_ucsctracks (BED file) contains MACS peaks file in text format.
Supplementary_files_format_and_content: 00DBGWU_K562_bigWig_URLs.txt (TXT file) contains peak shape information in the form of a signal histogram.
Supplementary_files_format_and_content: K562_ChIP-seq.xlsx (Excel file)

source_name: K562, ChIP fraction

extract_protocol:
Cell lysates were clarified from sonicated nuclei and the ARID4B-DNA complexes were isolated with the anti-ARID4B antibody (CAT#: A302-233A, LOT#: A302-233A-1, Bethyl Laboratories).
Libraries were prepared for sequencing using standard Illumina protocols.

value: Erythroleukemic cell line

tag: chip antibody

value: anti-ARID4B antibody (CAT#:A302-233A, LOT#:A302-233A-1,Bethyl Laboratories)


title: K562 Input control

source_name: K562, input


title: WT-1

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

description:
SY061_TGACCA
60 million paired-end reads performed at Columbia University Genome Center

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR

extract_protocol: NOT PROVIDED; REQUESTED

tag: genotype

value: SF3B1 wild type knock-in


title: IMCD negdeprived

city: St. Louis

first: Leslie

middle: Stuart

last: Gewin

state: MO

address: 660 S Euclid Ave, McDonnell Science Building, Rm 718

department: Medicine (Nephrology)

institute: Washington University in St. Louis

data_processing:
RNAseq raw reads were aligned against MM10 reference using TOPHAT2 followed by gene quantification into FPKM using Cufflinks. .
Differential expression analyses were performed using cuffdiff from Cufflink packages.
p values were adjusted using Benjamini-Hochberg method.
Supplementary_files_format_and_content: Processed data are comparisons between different samples in Excel files

source_name: IMCD (inner medullary collecting duct) cells

growth_protocol: IMCD cells immortalized with psv40 as detailed and characterized in JASN manuscript, PMID 20576806

extract_protocol:
RNA isolation performed with Qiagen Rneasy Kit plus DNAse step
performed by Vanderbilt VANTAGE Core
RNAseq with Hiseq 2500 with 50 bp, 30 million reads

treatment_protocol: Cells were either kept in serum containing media or serum starved prior to isolation

value: C57B/l mice with Tgfbr2 floxed

tag: cre treatment

value: Untreated

tag: tgfbr2 expression

tag: media conditions

value: Serum deplete for 4 days


title: WT-2

description:
SY062_ACAGTG
60 million paired-end reads performed at Columbia University Genome Center


title: SF3B1_mutant-1

description:
SY063_GCCAAT
60 million paired-end reads performed at Columbia University Genome Center

value: SF3B1 K700E


title: WT_CD4+ T

data_processing:
FASTQ demultiplexing with CellRanger v3.1.0
Read alignment and single cell data parsing with CellRanger v3.1.0
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files

source_name: CNS infiltrated CD4+ T cells

growth_protocol: WT or Tnfr2-/- mice were immunized with MOG(35-55) peptide and CD4+ T cells were isolated at day 15 from the CNS of WT and Tnfr2-/- mice followed by single cell RNA sequencing by 10X genomics.

extract_protocol:
CNS infiltrated CD4+ T cells were purified by flow cytometry sorting and performed single cell sequencing.
10x Genomics Chromium Single Cell 3' v3

treatment_protocol: Mice were immunized with MOG emulsion (Hookie kit, Cat#EK-2160) subcutaneously 0.1 ml each in both upper and lower back. 3 hrs after immunization pertussis toxin was injected intraperitoneally.

value: CD4+ T cells isolated from spinal cord

value: WT