title: 21T2_5

value: astrocyte


title: R14-EV-Kidney-12M_TCRB

status: Public on Feb 10 2025

type: SRA

city: Chicago

first: James

last: Mathew

state: IL

address: 300 E Superior

department: Department of Surgery, Division of Organ Transplantation, Comprehensive Transplant Center

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Library name: R14-EV-Kidney-12M_TCRB

library_source: genomic

data_processing:
raw data preprocessed by Adaptive Biotechnologies
Assembly: hg18 (NCBI 36)
Supplementary files format and content: sample level TSV files (unique per sample) are tab deliminated and contain the T-cell receptor rearrangement sequences, their observed counts and frequencies in the sample, as well as information relating to rearrangement length, V,D,J gene usage and their respective indices along the nucleotide rearrangement, and whether the sequence was in frame for transcription/translation and thus productive
Supplementary files format and content: project level TSV file (one containing data from all samples) is tab deliminated and contains sample level metrics including the numbers of T-cell receptor rearrangements and templates observed, the total number of nucleated cells observed, the T-cell content of the sample i.e. the fraction of T-cell templates observed divided by the total number of nucleated cells observed, the fraction of T-cell receptors that are productive or in-frame, Simpson clonality of the observed productive T-cells, the sequencing locus TCRB, and the estimated gDNA mass sequenced
Library strategy: TCR-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
QIAamp DNA blood Mini kit (Qiagen)
Bias-controlled multiplex PCR using forward and reverse primers specific to CDR3 Vβ and Jβ region (Adaptive Biotechnologies)

tag: tissue

value: Kidney

tag: subject

tag: visit

value: 12 Month

tag: diagnosis 3_months

value: Stable

tag: induction

value: Campath


title: R14-EV-Kidney-3M_TCRB

description: Library name: R14-EV-Kidney-3M_TCRB

value: 3 Month


title: R14-EV-Kidney-PreTx_TCRB

description: Library name: R14-EV-Kidney-PreTx_TCRB

value: PreTx


title: R14-EV-CD8-DRTC_TCRB

description: Library name: R14-EV-CD8-DRTC_TCRB

source_name: DRTC

value: DRTC


title: R13-EV-Urine_Pellet-3M_TCRB

description: Library name: R13-EV-Urine_Pellet-3M_TCRB

source_name: Urine Pellet

value: Urine Pellet


title: R13-EV-PBMC-PreTx_TCRB

description: Library name: R13-EV-PBMC-PreTx_TCRB

source_name: PBMC

value: PBMC


title: R13-EV-Kidney-12M_TCRB

description: Library name: R13-EV-Kidney-12M_TCRB


title: 21T2_1

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

country: Germany

institute: Helmholtz Zentrum

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the GRCm38.101 reference genome using STAR software version 2.6.0a.
TPM expression values based on ENSEMBL annotation version GRCm38.92 were calculated with RSEM (1.3.0).
Assembly: mm10
Supplementary files format and content: txt file

molecule: polyA RNA

organism: Mus musculus

source_name: brain

growth_protocol: Transgenic mice were fed ad libitum

extract_protocol:
Single cells were sucked with an electrophysiological tip and transfer to tube for subsequent analysis.
SmartSeq2 + illumina protocols

treatment_protocol: Transgenic mice were injected with Mok-LV carrying the gRNA targeting Sox9 or Trps1 or both

value: brain

tag: cell type

tag: grna

tag: day

tag: batch


title: AG4_b5

value: no-gRNA

value: Adult


title: PX43_5h_3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Library name: HSOC_PX43_5h_3

data_processing:
Raw sequencing data was pseudo-aligned against the human transcriptome (Ensembl GRCh38.105) using kallisto (v0.45.0) with 20 bootstraps. Gene expression was summarized from the scaledTPM values of the transcripts using tximport (v1.30.0).
Assembly: Ensembl GRCh38 version 105.
Supplementary files format and content: Excel file with scaled TPM values summarized to gene expression using tximport (v1.30.0).

molecule: total RNA

source_name: human skin

growth_protocol: Human skin samples were incubated at 37°C in a humidified atmosphere with 5% CO₂ for up to 24 hours.

extract_protocol:
Basal keratinocytes were isolated for RNA extraction and sequencing using microdissection under an Olympus stereomicroscope. RNA was then extracted using the innuPREP RNA Mini Kit 2.0.
Illumina TruSeq Stranded Total RNA Library Prep Kit with RiboZero Plus rRNA depletion.

treatment_protocol: The human skin was injected with either 85 µg of PX43 produced in Escherichia coli,  85 µg human IgG, 85 µg  AK23, or 85  µg  mIgG.

value: human skin

value: Basal Human Keratinocytes

tag: treatment

tag: time

tag: replicate

value: replicate 3


title: R13-EV-Kidney-3M_TCRB

description: Library name: R13-EV-Kidney-3M_TCRB


title: 15R-CD8-DRTCs

description: Library name: 15R-CD8-DRTCs

value: campath


title: R14-EV-PBMC-PreTx_TCRB

description: Library name: R14-EV-PBMC-PreTx_TCRB


title: PX43_5h_4

description: Library name: HSOC_PX43_5h_4

value: replicate 4


title: R13-EV-Kidney-PreTx_TCRB

description: Library name: R13-EV-Kidney-PreTx_TCRB

value: Kidney


title: R13-EV-CD4-DRTC_TCRB

description: Library name: R13-EV-CD4-DRTC_TCRB


title: R14-EV-CD4-DRTC_TCRB

description: Library name: R14-EV-CD4-DRTC_TCRB


title: AG3_b5

value: astrocyte


title: R13-EV-CD8-DRTC_TCRB

description: Library name: R13-EV-CD8-DRTC_TCRB

value: Stable


title: PX43_5h_2

description: Library name: HSOC_PX43_5h_2

value: replicate 2


title: 13R-Urine-pellet-12-Month_TCRB

description: Library name: 13R-Urine-pellet-12-Month_TCRB

value: 12 Month

value: Borderline

value: Simulect


title: 13R-Urine-pellet-6-Month_TCRB

description: Library name: 13R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month


title: AG11_b5

value: brain


title: PX43_5h_5

description: Library name: HSOC_PX43_5h_5

value: replicate 5


title: AG7_b5

value: no-gRNA

value: Adult


title: 13R-Urine-pellet-3-Month_TCRB

description: Library name: 13R-Urine-pellet-3-Month_TCRB

value: 3 Month


title: AG10_b5


title: AK23_5h_6

description: Library name: HSOC_AK23_5h_6

value: human skin

value: Basal Human Keratinocytes

value: replicate 6


title: 13R-PBMC-12-Month_TCRB

description: Library name: 13R-PBMC-12-Month_TCRB

value: PBMC


title: R13-EV-PBMC-12M_TCRB

description: Library name: R13-EV-PBMC-12M_TCRB

value: Campath


title: 13R-PBMC-3-Month_TCRB

description: Library name: 13R-PBMC-3-Month_TCRB


title: 13R-PBMC-6-Month_TCRB

description: Library name: 13R-PBMC-6-Month_TCRB


title: 13R-PBMC-PreTx_TCRB

description: Library name: 13R-PBMC-PreTx_TCRB

value: PreTx


title: AG1_b5

value: astrocyte


title: AK23_5h_5

description: Library name: HSOC_AK23_5h_5


title: AK23_5h_4

description: Library name: HSOC_AK23_5h_4

value: replicate 4


title: AG8_b5


title: AK23_5h_2

description: Library name: HSOC_AK23_5h_2

value: replicate 2


title: R12-EV-Urine_Pellet-12M_TCRB

description: Library name: R12-EV-Urine_Pellet-12M_TCRB

value: 12 Month

value: Reject

tag: rejection episode

value: Rejection 2


title: AK23_5h_3

description: Library name: HSOC_AK23_5h_3

value: replicate 3


title: AG2_b5

value: brain


title: R12-EV-Urine_Pellet-3M_TCRB

description: Library name: R12-EV-Urine_Pellet-3M_TCRB

value: Urine Pellet

value: Rejection 1


title: 21T_11


title: R12-EV-Urine_Pellet-2W_TCRB

description: Library name: R12-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: 21T_10


description: Library name: R12-EV-Urine_Pellet-for_cause_May_14_2019_TCRB

value: 8 Month


title: PX43_5h_1

description: Library name: HSOC_PX43_5h_1

value: human skin

value: Basal Human Keratinocytes

value: replicate 1


title: NA_0h_5

description: Library name: HSOC_NA_0h_5

value: NoAb

value: replicate 5


title: R12-EV-Kidney-12M_TCRB

description: Library name: R12-EV-Kidney-12M_TCRB

value: Kidney

value: Campath


title: AK23_5h_1

description: Library name: HSOC_AK23_5h_1


title: NA_0h_4

description: Library name: HSOC_NA_0h_4

value: replicate 4


description: Library name: R12-EV-Kidney-for_cause_May_14_2019_TCRB


title: 21T_8_b4

value: astrocyte


title: NA_0h_6

description: Library name: HSOC_NA_0h_6

value: replicate 6


title: 13R-CD8-DRTCs

description: Library name: 13R-CD8-DRTCs

value: DRTC

value: Borderline

value: Simulect


title: 13R-kidney-3-Month_TCRB

description: Library name: 13R-kidney-3-Month_TCRB

value: 3 Month


title: R12-EV-PBMC-12M_TCRB

description: Library name: R12-EV-PBMC-12M_TCRB

value: PBMC

value: 12 Month

value: Reject

value: Rejection 2


title: 13R-kidney-PreTx_TCRB

description: Library name: 13R-kidney-PreTx_TCRB

value: PreTx


title: R12-EV-PBMC-for_cause_May_14_2019_TCRB

description: Library name: R12-EV-PBMC-for_cause_May_14_2019_TCRB

value: 8 Month


title: NA_0h_3

description: Library name: HSOC_NA_0h_3

value: human skin

value: Basal Human Keratinocytes

value: NoAb

value: replicate 3


title: 21T_7_b4

value: brain


title: NA_0h_2

description: Library name: HSOC_NA_0h_2

value: replicate 2


title: R12-EV-Kidney-PreTx_TCRB

description: Library name: R12-EV-Kidney-PreTx_TCRB

value: Kidney

value: Campath


title: 21T_6_b4

value: astrocyte


title: R12-EV-Kidney-3M_TCRB

description: Library name: R12-EV-Kidney-3M_TCRB

value: Rejection 1


title: 10R-Urine-pellet-12-Month_TCRB

description: Library name: 10R-Urine-pellet-12-Month_TCRB

value: Urine Pellet

value: Borderline

value: Simulect


title: NA_0h_1

description: Library name: HSOC_NA_0h_1

value: replicate 1


title: 21T_12


title: 21T_9_b4


title: R12-EV-CD8-DRTC_TCRB

description: Library name: R12-EV-CD8-DRTC_TCRB

value: DRTC

value: Reject


title: 10R-Urine-pellet-3-Month_TCRB

description: Library name: 10R-Urine-pellet-3-Month_TCRB

value: 3 Month


title: 10R-PBMC-PreTx_TCRB

description: Library name: 10R-PBMC-PreTx_TCRB

value: PBMC

value: PreTx


title: 10R-kidney-3-Month_TCRB

description: Library name: 10R-kidney-3-Month_TCRB


title: R12-EV-CD4-DRTC_TCRB

description: Library name: R12-EV-CD4-DRTC_TCRB


title: 21T_1_b4


title: 10R-CD8-DRTCs

description: Library name: 10R-CD8-DRTCs


title: 10R-CD4-DRTCs

description: Library name: 10R-CD4-DRTCs


title: 09R-Urine-pellet-12-Month_TCRB

description: Library name: 09R-Urine-pellet-12-Month_TCRB

value: 12 Month

value: campath


title: GEX+ADT of Pool3 GEM3

city: Heidelberg

first: Alexandra

middle: M

last: Poos

address: Im Neuenheimer Feld 410

institute: University Hospital Heidelberg

description:
Library name: Po3C3_GEX_ADT
patient sample
10X Genomics

library_source: other

data_processing:
CellRanger multi (v7.0.0) was used for the alignment of demultiplexed libraries to reference genome GRCh38 (refdata-gex-GRCh38-2020-A) and the generation of the feature barcode matrices. For the TCR libraries, reference refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 was used. The count matrices were loaded into R (v4.2.2) by using the standard Seurat (v5.0.1) parameters. The feature_reference.csv file is similar for all pools and channels. The file Hashing_information.txt includes all information for sample identification.
Assembly: GRCh38
Supplementary files format and content: CellRanger output GEX+ADT: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output TCR: filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: other

source_name: bone marrow

extract_protocol:
Cryopreserved samples were thawed at 37ºC, resuspended in 10 mL RPMI with 10% FCS, and centrifuged at 300 g for 5 min. The pellet was resuspended in 10 mL RPMI with 10% FCS. Cells were centrifuged at 300 g for 5 min, and the pellet resuspended in 50-100 µL PBS plus Calcein (0.1 µM 1:100 from 10µM diluted stock) and efluor-506 fixable viability dye (eBioscience, 1:1000). After 5 min at RT, 100-200 µL antibody master mix for FACS sorting (Table S3) were added. Individual samples were hashed by adding 0.1 µg TotalSeq of the respective anti-human Hashtag 1-4 and 6-9 (Biolegend). After 15 min at 4ºC, 5 mL FACS buffer (1 x DPBS, 5% FCS, 0.5 mM EDTA) was added and the tube centrifuged at 300 g for 5 min, and the pellet resuspended in 300 µL FACS buffer. Sorting was performed with a BD FACS Aria. Gating strategy is shown in Fig. S5A. For each cell population and sample, a maximum of 10,000 events (range=3500-10000 per population, CD90+CD34+ all cells) were sorted into 1.5 mL Protein low binding Eppendorf tubes prefilled with 150 µL Cell Staining Buffer (Biolegend). Sorted cells were pooled into batches, where paired samples from the same patient were in different batches. Each batch contained approx. 130,000 sorted cells, which were centrifuged at 300 g for 5 min and the pellet resuspended in 25 µL Cell Staining Buffer. Subsequently, 2.5 µL of Human TruStain FcX Blocking reagent (Biolegend) was added to the pooled cell suspension and incubated for 10 min at 4ºC. After adding 25 µL of reconstituted TotalSeq™-C antibody cocktail (Biolegend), cells were incubated for 30 min at 4ºC.Cells were washed 3x with 3.5 mL Cell Staining Buffer and resuspended in PBS and loaded onto three 10x GEMs (22,000-24,000 cells per GEM) per batch.
Immunoprofiling was performed according to the Chromium Next GEM Single Cell 5ʹ Reagent Kit v2 (Dual Index) user guide with feature barcode technology for cell surface protein & immune receptor mapping (10x Genomics; CG000330 Rev A). Generated gene expression (GEX) and protein (ADT) libraries were paired-end sequenced on the NovaSeq 6000 S4. Generated V(D)J libraries were paired-end sequenced on the NextSeq 550.

value: bone marrow

value: sorted myeloma+microenvironment cells


title: 21T_5_b4

value: brain


title: R12-EV-PBMC-PreTx_TCRB

description: Library name: R12-EV-PBMC-PreTx_TCRB

value: Campath


title: 10R-Urine-pellet-6-Month_TCRB

description: Library name: 10R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: 09R-PBMC-6-Month_TCRB

description: Library name: 09R-PBMC-6-Month_TCRB


title: GEX+ADT of Pool3 GEM1

description:
Library name: Po3C1_GEX_ADT
patient sample
10X Genomics


title: preprocessed Seurat object of the microenvironment cells of P01-P05

description:
Library name: Seurat_BME
patient sample
10X Genomics

value: sorted microenvironment cells


title: 10R-PBMC-6-Month_TCRB

description: Library name: 10R-PBMC-6-Month_TCRB


title: preprocessed Seurat object of the Plasma cells of P01-P05

description:
Library name: Seurat_PlasmaCells
patient sample
10X Genomics

value: sorted myeloma cells


title: 21T_4_b4

value: astrocyte


title: 21T_3_b4


title: 10R-kidney-12-Month_TCRB

description: Library name: 10R-kidney-12-Month_TCRB

value: Kidney

value: Borderline

value: Simulect


title: 21T_2_b4


title: 10R-PBMC-12-Month_TCRB

description: Library name: 10R-PBMC-12-Month_TCRB


title: GEX+ADT of Pool4 GEM6

description:
Library name: Po4C6_GEX_ADT
patient sample
10X Genomics


title: 09R-kidney-12-Month_TCRB

description: Library name: 09R-kidney-12-Month_TCRB


title: GEX+ADT of Pool4 GEM5

description:
Library name: Po4C5_GEX_ADT
patient sample
10X Genomics


title: 10R-kidney-PreTx_TCRB

description: Library name: 10R-kidney-PreTx_TCRB


title: 09R-PBMC-PreTx_TCRB

description: Library name: 09R-PBMC-PreTx_TCRB


title: GEX+ADT of Pool4 GEM4

description:
Library name: Po4C4_GEX_ADT
patient sample
10X Genomics


title: 09R-Urine-pellet-2-week_TCRB

description: Library name: 09R-Urine-pellet-2-week_TCRB

value: Urine Pellet

value: 2 Week


title: 7T2_15


title: GEX+ADT of Pool3 GEM2

description:
Library name: Po3C2_GEX_ADT
patient sample
10X Genomics


title: 09R-Urine-pellet-6-Month_TCRB

description: Library name: 09R-Urine-pellet-6-Month_TCRB


title: 7T2_14


title: 09R-PBMC-12-Month_TCRB

description: Library name: 09R-PBMC-12-Month_TCRB

value: PBMC


title: 7T2_13


title: R08-EV-Urine_Pellet-12M_TCRB

description: Library name: R08-EV-Urine_Pellet-12M_TCRB

value: Stable


title: 09R-CD4-DRTCs

description: Library name: 09R-CD4-DRTCs

value: DRTC


title: 7T2_9


title: GEX+ADT of Pool2 GEM6

description:
Library name: Po2C6_GEX_ADT
patient sample
10X Genomics


title: GEX+ADT of Pool1 GEM3

description:
Library name: Po1C3_GEX_ADT
patient sample
10X Genomics


title: R08-EV-Urine_Pellet-3M_TCRB

description: Library name: R08-EV-Urine_Pellet-3M_TCRB

value: 3 Month


title: R08-EV-PBMC-12M_TCRB

description: Library name: R08-EV-PBMC-12M_TCRB

value: 12 Month


title: 09R-PBMC-3-Month_TCRB

description: Library name: 09R-PBMC-3-Month_TCRB

value: campath


title: GEX+ADT of Pool1 GEM2

description:
Library name: Po1C2_GEX_ADT
patient sample
10X Genomics

value: bone marrow

value: sorted myeloma+microenvironment cells


title: 7T2_12

value: brain


title: 09R-kidney-3-Month_TCRB

description: Library name: 09R-kidney-3-Month_TCRB


title: 7T2_11


title: 09R-kidney-PreTx_TCRB

description: Library name: 09R-kidney-PreTx_TCRB

value: PreTx


title: GEX+ADT of Pool2 GEM5

description:
Library name: Po2C5_GEX_ADT
patient sample
10X Genomics


title: R08-EV-Kidney-12M_TCRB

description: Library name: R08-EV-Kidney-12M_TCRB

value: Campath


title: R08-EV-PBMC-PreTx_TCRB

description: Library name: R08-EV-PBMC-PreTx_TCRB


title: GEX+ADT of Pool1 GEM1

description:
Library name: Po1C1_GEX_ADT
patient sample
10X Genomics


title: 09R-CD8-DRTCs

description: Library name: 09R-CD8-DRTCs


title: GEX+ADT of Pool2 GEM4

description:
Library name: Po2C4_GEX_ADT
patient sample
10X Genomics


title: 7T2_10

value: astrocyte


title: 7T2_6


title: Thumpd Knockout Replicate 2

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: ThumpdKO_2

data_processing:
6 RNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina® Stranded Total RNA Prep. Ligation was done with Ribo-Zero Plus and paired-end sequencing.
RNA-Seq FASTQ files were aligned to the reference genome using STAR using the 2-pass setting.
Raw counts were produced using RSEM.
Downstream analysis presented in the manuscript was done using Limma and fgsea.
Assembly: hg38 with the GENCODE_46 GTF
Supplementary files format and content: Tab-delimited file containing RSEM raw counts for the Thumpd1 WT & KO samples used in this study.

source_name: kidney

growth_protocol: HEK-293T (WT and THUMPD1 KO) cells were grown in DMEM media at 37˚C

extract_protocol:
Total RNA was isolated by Trizol extraction
Total RNA from HEK-293T cells in which the THUMPD1 gene has been knocked out (THUMPD1 KO) vs control (WT) were isolated by Trizol extraction and sequenced on NovaSeq 6000 S1 using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

value: kidney

tag: cell line

value: immortalized

tag: genotype

value: Thumpd-/-


title: 7T2_8


title: R08-EV-Urine_Pellet-2W_TCRB

description: Library name: R08-EV-Urine_Pellet-2W_TCRB

value: Urine Pellet


title: R08-EV-CD4-DRTC_TCRB

description: Library name: R08-EV-CD4-DRTC_TCRB


title: 7T2_4


title: 08R-Urine-pellet-6-Month_TCRB

description: Library name: 08R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: R08-EV-PBMC-3M_TCRB

description: Library name: R08-EV-PBMC-3M_TCRB

value: PBMC


title: Thumpd Knockout Replicate 1

description: Library name: ThumpdKO_1


title: R08-EV-Kidney-3M_TCRB

description: Library name: R08-EV-Kidney-3M_TCRB

value: Kidney

value: Stable


title: 7T2_7


title: 08R-Urine-pellet-3-Month_TCRB

description: Library name: 08R-Urine-pellet-3-Month_TCRB

value: 3 Month


title: Thumpd Knockout Replicate 3

description: Library name: ThumpdKO_3


title: 7T2_5


title: R08-EV-CD8-DRTC_TCRB

description: Library name: R08-EV-CD8-DRTC_TCRB

value: DRTC


title: 08R-PBMC-12-Month_TCRB

description: Library name: 08R-PBMC-12-Month_TCRB

value: 12 Month


title: Thumpd Wildtype Replicate 3

description: Library name: ThumpdWT_3

value: Thumpd+/+


title: 08R-PBMC-6-Month_TCRB

description: Library name: 08R-PBMC-6-Month_TCRB


title: 7T2_2


title: 08R-PBMC-3-Month_TCRB

description: Library name: 08R-PBMC-3-Month_TCRB


title: 08R-PBMC-PreTx_TCRB

description: Library name: 08R-PBMC-PreTx_TCRB


title: 7T2_3


title: 13R-CD4-DRTCs

description: Library name: 13R-CD4-DRTCs

value: Borderline

value: Simulect


title: 08R-kidney-12-Month_TCRB

description: Library name: 08R-kidney-12-Month_TCRB


title: 08R-kidney-3-Month_TCRB

description: Library name: 08R-kidney-3-Month_TCRB


title: 08R-Urine-pellet-2-week_TCRB

description: Library name: 08R-Urine-pellet-2-week_TCRB

value: 2 Week


title: 7T_16

value: brain


title: 7T2_1

value: astrocyte


title: 08R-kidney-PreTx_TCRB

description: Library name: 08R-kidney-PreTx_TCRB

value: PreTx

value: Campath


title: Thumpd Wildtype Replicate 1

description: Library name: ThumpdWT_1

value: kidney

value: immortalized


title: Thumpd Wildtype Replicate 2

description: Library name: ThumpdWT_2


title: 08R-CD8-DRTCs

description: Library name: 08R-CD8-DRTCs


title: 83, OE-3 group

city: Chengdu

first: Juan

last: Wu

state: Sichuan

address: No. 37 Guo Xue Alley, Wuhou District

department: Anesthesiology

country: China

institute: West China Hospital of Sichuan University

data_processing:
CLC Genomics Workbench v11.0.1
Sequences reads were trimmed for adaptor sequence/low-quality sequence by CLC genomic benchwork (parameters-Quality limit :0.05)
Assembly: mm 10
Supplementary files format and content: tab-delimited text files includ FPKM values for each samples

source_name: 83 cell line

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

value: 83 cell line

value: overexpression of ApoD


title: 83, OE-2 group


title: 08R-CD4-DRTCs

description: Library name: 08R-CD4-DRTCs


title: R07-EV-PBMC-PreTx_TCRB

description: Library name: R07-EV-PBMC-PreTx_TCRB

value: PBMC

value: campath


title: R07-EV-PBMC-12M_TCRB

description: Library name: R07-EV-PBMC-12M_TCRB

value: Stable


title: 7T_11


title: R07-EV-Kidney-12M_TCRB

description: Library name: R07-EV-Kidney-12M_TCRB

value: Kidney


title: 7T_14


title: 83, OE-1 group


title: 83, NC-1 group

value: control


title: R07-EV-CD4-DRTC_TCRB

description: Library name: R07-EV-CD4-DRTC_TCRB

value: DRTC


title: 7T_9


title: R07-EV-Urine_Pellet-12M_TCRB

description: Library name: R07-EV-Urine_Pellet-12M_TCRB

value: Urine Pellet

value: 12 Month


title: 7,OlS-shACSS2 H3K27ac ChlP

city: Shanghai

first: Pingyu

last: Liu

address: 2005 Songhu Rd

institute: Human Phenome Institute, Fudan University

data_processing:
Quality control of sequencing readings were performed by using FastQC v0.12.1.
Sequencing reads were aligned to human(hg38) and Drosophila(BDGP6) genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely mapping reads were retained.
Peaks for ChIP-seq data were called using MACS v2.2.7 with the sinificance q value<=0.05.
Assembly: hg38(human),BDGP6(Drosophila)
Supplementary files format and content: bigWig

source_name: Human embryonic lung fibroblasts

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature, quenched with 2.5 M glycine. After cell lysis, chromatin was fragmented using Bioruptor (Diagenode).
The ChIP-Seq library preparation was proceeded as follows:
(1) The DNA fragments were end-repaired and A-tailed.
(2) The DNA fragments with A tail were ligated with sequencing adaptors.
(3) The final DNA library was obtained after size selection and PCR amplification.
Libraries were analyzed for size distribution by Agilent 5400 system（Agilent, USA）and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to the effective library concentration and data amount required.

value: Human embryonic lung fibroblasts

value: ACSS2 knockdown


title: 7T_15

value: brain

value: astrocyte


title: R07-EV-Urine_Pellet-3M_TCRB

description: Library name: R07-EV-Urine_Pellet-3M_TCRB

value: 3 Month


title: R05-EV-Urine_Pellet-12M_TCRB

description: Library name: R05-EV-Urine_Pellet-12M_TCRB

value: Campath


title: R05-EV-Urine_Pellet-3M_TCRB

description: Library name: R05-EV-Urine_Pellet-3M_TCRB


title: 7T_13


title: 5,Pro-H3K27ac ChIP

value: WT


title: R07-EV-Urine_Pellet-2W_TCRB

description: Library name: R07-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: R05-EV-PBMC-12M_TCRB

description: Library name: R05-EV-PBMC-12M_TCRB


title: 83, NC-3 group

value: 83 cell line


title: 7T_12


title: 3,OlS-shACSS2-input


title: R05-EV-PBMC-3M_TCRB

description: Library name: R05-EV-PBMC-3M_TCRB

value: PBMC


title: R07-EV-CD8-DRTC_TCRB

description: Library name: R07-EV-CD8-DRTC_TCRB

value: campath


title: 7T_7


title: 7T_6


title: 2,OlS-input

value: Scramble


title: 83, NC-2 group


title: R05-EV-Kidney-3M_TCRB

description: Library name: R05-EV-Kidney-3M_TCRB

value: Kidney

value: Stable


title: IMR90 cells, sen-shACSS2-3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to hg 38 using CLC genomic benchwok (parameters- mismath cost:2 inserion cost:3 deleton cost:3 Lengh fraction:0.8 similarity fration:0.8)
Read count extraction and normalization were performed usina CLC genomic benchwork
Assembly: hg 38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: sen


title: 7T_3


title: R07-EV-Kidney-3M_TCRB

description: Library name: R07-EV-Kidney-3M_TCRB


title: R07-EV-Kidney-PreTx_TCRB

description: Library name: R07-EV-Kidney-PreTx_TCRB

value: PreTx


title: 7T_10


title: R04-EV-Urine_Pellet-2W_TCRB

description: Library name: R04-EV-Urine_Pellet-2W_TCRB

value: Urine Pellet

value: Borderline


title: IMR90 cells, sen-shACSS2-1

value: Human embryonic lung fibroblasts

value: ACSS2 knockdown


title: R04-EV-PBMC-12M_TCRB

description: Library name: R04-EV-PBMC-12M_TCRB

value: 12 Month


title: 6,OlS-H3K27ac ChlP


title: 7T_8

value: brain

value: astrocyte


title: 7T_1


title: 21C19_slice-ctrl

value: in-slice control


title: R04-EV-PBMC-PreTx_TCRB

description: Library name: R04-EV-PBMC-PreTx_TCRB

value: Campath


title: IMR90 cells, sen-3


title: R04-EV-Urine_Pellet-12M_TCRB

description: Library name: R04-EV-Urine_Pellet-12M_TCRB


title: R07-EV-PBMC-3M_TCRB

description: Library name: R07-EV-PBMC-3M_TCRB

value: 3 Month


title: IMR90 cells, sen-2


title: R05-EV-PBMC-PreTx_TCRB

description: Library name: R05-EV-PBMC-PreTx_TCRB

value: PBMC


title: R03-EV-Urine_Pellet-12M_TCRB

description: Library name: R03-EV-Urine_Pellet-12M_TCRB

value: campath


title: R05-EV-Kidney-12M_TCRB

description: Library name: R05-EV-Kidney-12M_TCRB


title: R03-EV-Urine_Pellet-3M_TCRB

description: Library name: R03-EV-Urine_Pellet-3M_TCRB


title: R03-EV-Urine_Pellet-2W_TCRB

description: Library name: R03-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: 7T_5


title: R05-EV-Kidney-PreTx_TCRB

description: Library name: R05-EV-Kidney-PreTx_TCRB

value: Kidney


title: 1,Pro-input

value: WT


title: R05-EV-CD8-DRTC_TCRB

description: Library name: R05-EV-CD8-DRTC_TCRB

value: DRTC

value: Stable


title: 7T_4


title: R05-EV-Urine_Pellet-2W_TCRB

description: Library name: R05-EV-Urine_Pellet-2W_TCRB

value: Urine Pellet


title: R05-EV-CD4-DRTC_TCRB

description: Library name: R05-EV-CD4-DRTC_TCRB


title: R04-EV-Urine_Pellet-3M_TCRB

description: Library name: R04-EV-Urine_Pellet-3M_TCRB

value: Borderline


title: IMR90 cells, sen-shACSS2-2

value: Human embryonic lung fibroblasts

value: sen


title: 7T_2


title: IMR90 cells, sen-1

value: Scramble


title: R04-EV-PBMC-3M_TCRB

description: Library name: R04-EV-PBMC-3M_TCRB


title: R04-EV-Kidney-PreTx_TCRB

description: Library name: R04-EV-Kidney-PreTx_TCRB

value: PreTx


title: R03-EV-Kidney-3M_TCRB

description: Library name: R03-EV-Kidney-3M_TCRB


title: IMR90 cells, pro-3

value: pro


title: R04-EV-CD8-DRTC_TCRB

description: Library name: R04-EV-CD8-DRTC_TCRB


title: 21C18_slice-ctrl

value: brain

value: in-slice control


title: 21C13

value: astrocyte

value: g-Control


title: R04-EV-CD4-DRTC_TCRB

description: Library name: R04-EV-CD4-DRTC_TCRB

value: Campath


title: R03-EV-PBMC-12M_TCRB

description: Library name: R03-EV-PBMC-12M_TCRB

value: PBMC

value: 12 Month

value: campath


title: R03-EV-PBMC-3M_TCRB

description: Library name: R03-EV-PBMC-3M_TCRB

value: 3 Month


title: 03R-Urine-pellet-12-Month_TCRB

description: Library name: 03R-Urine-pellet-12-Month_TCRB

value: Stable


title: 03R-Urine-pellet-6-Month_TCRB

description: Library name: 03R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month


title: 21C17


title: 21C16


title: WT_IgG_2

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

description: stable cell line

data_processing:
3' ends adapter sequences were removed using Trim Galore! (version 0.6.5) and Cutadapt (version 2.8).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 1000 bp (less than 1% of the total) were excluded from subsequent analysis.
To generate the signal landscape, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was multiplied by 1x10-6 divided by a library size. These values were then averaged over a 10 bp resolution and written in bigWig files.
For the bigWig files (v1), the library size is defined as the number of uniquely mapped fragments after deduplication. For the bigWig files (v2) specific to SNF2H, the library size is determined by the number of fragments mapped to the common peaks across the four SNF2H samples. These common peaks were identified by merging the peaks called in each individual sample compared to the IgG control using MACS (version 1.4.2) with a p-value cutoff of 1e-5 and a window size of 300 bp.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: LNCaP cells

growth_protocol: LNCaP human prostate cancer cells with SPOP W131G mutation CHD1 intact or CHD1 knockout were cultured  in RPMI 1640 medium with 10% Charcoal-Stripped FBS and 1% penicillin/streptomycin and incubated at 37 °C under 5% CO2.

extract_protocol:
CUT&RUN was carried out using the CUT&RUN Assay Kit (Cell Signaling Technology,86652) as per the manufacturer’s instructions
Sequencing libraries were prepared using the DNA Library Prep Kit (Cell Signaling Technology, 56795) for Illumina Platforms

value: LNCaP cells

value: human prostate cancer cells

value: SPOP W131G mutation

tag: cut&run antibody

value: IgG control (Cell Signaling Technology, 66362)


title: IMR90 cells, pro-2

value: Human embryonic lung fibroblasts

value: WT

value: pro


title: R03-EV-PBMC-PreTx_TCRB

description: Library name: R03-EV-PBMC-PreTx_TCRB

value: PreTx


title: 03R-Urine-pellet-3-Month_TCRB

description: Library name: 03R-Urine-pellet-3-Month_TCRB


title: IMR90 cells, pro-1


title: 21C15

value: brain

value: astrocyte

value: g-Control


title: R03-EV-Kidney-12M_TCRB

description: Library name: R03-EV-Kidney-12M_TCRB

value: Kidney

value: 12 Month


title: 21C10


title: 03R-PBMC-12-Month_TCRB

description: Library name: 03R-PBMC-12-Month_TCRB

value: PBMC

value: Campath


title: R03-EV-CD8-DRTC_TCRB

description: Library name: R03-EV-CD8-DRTC_TCRB

value: DRTC

value: Stable

value: campath


title: 21C14


title: WT_SNF2H_2

description: stable cell line

value: LNCaP cells

value: human prostate cancer cells

value: anti-SNF2h/ISWI (Bethyl, #A301-018A-T)


title: 03R-PBMC-PreTx_TCRB

description: Library name: 03R-PBMC-PreTx_TCRB


title: WT_CHD1_1

description: stable cell line

value: SPOP W131G mutation


title: R03-EV-CD4-DRTC_TCRB

description: Library name: R03-EV-CD4-DRTC_TCRB


title: 21C8


title: WT_SNF2H_1

description: stable cell line


title: 21C12


title: 21C7


title: 21C11


title: 03R-kidney-3-Month_TCRB

description: Library name: 03R-kidney-3-Month_TCRB

value: 3 Month


description: Library name: 03R-Urine-pellet--for-cause-mar25-19_TCRB

value: Urine Pellet

value: 6 Month


title: WT_IgG_1

description: stable cell line

value: IgG control (Cell Signaling Technology, 66362)


title: 03R-CD8-DRTCs

description: Library name: 03R-CD8-DRTCs


title: WT_CHD1_2

description: stable cell line


title: KO_SNF2H_1

description: stable cell line

value: SPOP W131G mutation CHD1 knockout


title: 03R-PBMC-3-Month_TCRB

description: Library name: 03R-PBMC-3-Month_TCRB


title: KO_IgG_2

description: stable cell line


title: 21C9

value: brain

value: astrocyte

value: g-Control


title: KO_SNF2H_2

description: stable cell line


title: 03R-kidney-PreTx_TCRB

description: Library name: 03R-kidney-PreTx_TCRB

value: Kidney

value: PreTx


title: 03R-kidney-12-Month_TCRB

description: Library name: 03R-kidney-12-Month_TCRB

value: 12 Month

value: Campath


title: R02-EV-Urine_Pellet-12M_TCRB

description: Library name: R02-EV-Urine_Pellet-12M_TCRB

value: Stable

value: campath


title: 21C6


title: 03R-Urine-pellet-2-week_TCRB

description: Library name: 03R-Urine-pellet-2-week_TCRB

value: 2 Week


title: R02-EV-Urine_Pellet-3M_TCRB

description: Library name: R02-EV-Urine_Pellet-3M_TCRB


title: 21C5


title: 03R-PBMC-6-Month_TCRB

description: Library name: 03R-PBMC-6-Month_TCRB

value: PBMC


title: KO_IgG_1

description: stable cell line

value: LNCaP cells

value: human prostate cancer cells


title: 21C4


title: R02-EV-Kidney-12M_TCRB

description: Library name: R02-EV-Kidney-12M_TCRB


title: R02-EV-PBMC-PreTx_TCRB

description: Library name: R02-EV-PBMC-PreTx_TCRB


title: Control

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: Background RNA associated with experiment

data_processing:
*library strategy: iCLIP
The reads from these libraries look as follows:
NNNNabcdNNNNxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxTGAGATCGGAAGAGCGGTTCAG
Where
NNNN is a four nucleotide degenerate sequence region. The first to these is to ensure high complexity sequence at the beginning, and the second - to serve as a reference for removing PCR duplications.
abcd is a four letter barcode:
xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx denotes the RNA fragmnet insert in the read.
The insert starts at position 13 (1-based) of the read
TGAGATCGGAAGAGCGGTTCAG sequence is common for all reads and should be immediately downstream of the insert."
3’ adapter were trimmed using Cutadapt (cutadapt -a TGAGATCGGAAGAGCGGTTCAG -m 28 -e 0.1 -u 4 --max n 5)
Trimmed sequencing were splitted by sample barcodes using FASTX. PCR diplicated were removed using in-house pipeline.
Sequencing reads were then mapped to hg38 using STAR (--outFilterMismatchNmax 2  --outFilterMultimapNmax 1)
Yodel (Lance E. Palmer et al, 2017) was used to define clusters in regions containing at least 10 reads in merged replicates
Assembly: hg38
Supplementary files format and content: WT clusters/bed
Supplementary files format and content: FA clusters/bed

source_name: HEK293 Flp-In Rbfox2 KO#7

growth_protocol: Cells were cultured in DMEM + 10% FBS and were around 80-90% confluent when harvested.

extract_protocol: A modified version of the iCLIP library preparation protocol outlined in Damianov et al., 2016 was followed. Briefly, L3 linker was ligated to the RNAs and samples were reverse transcriped with primers containing unique 4 nucleotide molecular identifiers for downstream PCR de-duplication. The cDNA was then size selected for molecules containing inserts between 20-80 nucleotides. cDNA was then circuliarzed with circligase and linearized with BamHI. Libraries were then prepared with PCR amplification using P5solexa and P3solexa primers. The products were run on an agarose gel and size selected.

value: HEK293 Flp-In Rbfox2 KO#7

value: Control

tag: barcode


title: R02-EV-Kidney-3M_TCRB

description: Library name: R02-EV-Kidney-3M_TCRB

tag: tissue

value: 3 Month


title: 21C3


title: Rbfox1(F125A)2

description:
Nuclease-protected RNA associated with Rbfox1(F125)/LASR replicate 2
FA_clusters_in_protein_coding_introns.bed


title: R02-EV-CD4-DRTC_TCRB

description: Library name: R02-EV-CD4-DRTC_TCRB

value: DRTC

tag: subject


title: R02-EV-CD8-DRTC_TCRB

description: Library name: R02-EV-CD8-DRTC_TCRB

tag: visit


title: 21C1

value: brain


title: 02R-Urine-pellet-6-Month_TCRB

description: Library name: 02R-Urine-pellet-6-Month_TCRB

value: Urine Pellet

value: 6 Month

tag: diagnosis 3_months

value: Borderline


title: 02R-Urine-pellet-12-Month_TCRB

description: Library name: 02R-Urine-pellet-12-Month_TCRB

tag: induction


title: Rbfox1(F125A)1

description:
Nuclease-protected RNA associated with Rbfox1(F125)/LASR replicate 1
FA_clusters_in_protein_coding_introns.bed


title: 03R-CD4-DRTCs

description: Library name: 03R-CD4-DRTCs


title: Rbfox1(WT)3

description:
Nuclease-protected RNA associated with Rbfox1(WT)/LASR replicate 3
WT_clusters_in_protein_coding_introns.bed


title: 21C2

tag: cell type

value: astrocyte

value: g-Control


title: 02R-Urine-pellet-2-week_TCRB

description: Library name: 02R-Urine-pellet-2-week_TCRB

value: Campath


title: 21ST_14

tag: grna


title: Rbfox1(WT)2

description:
Nuclease-protected RNA associated with Rbfox1(WT)/LASR replicate 2
WT_clusters_in_protein_coding_introns.bed


title: 02R-PBMC-6-Month_TCRB

description: Library name: 02R-PBMC-6-Month_TCRB


title: 02R-Urine-pellet-3-Month_TCRB

description: Library name: 02R-Urine-pellet-3-Month_TCRB


title: 21ST_13

tag: day


title: Rbfox1(WT)1

description:
Nuclease-protected RNA associated with Rbfox1(WT)/LASR replicate 1
WT_clusters_in_protein_coding_introns.bed


title: R02-EV-PBMC-3M_TCRB

description: Library name: R02-EV-PBMC-3M_TCRB

value: Stable


title: 02R-PBMC-3-Month_TCRB

description: Library name: 02R-PBMC-3-Month_TCRB


title: 02R-PBMC-PreTx_TCRB

description: Library name: 02R-PBMC-PreTx_TCRB

value: PreTx


title: 02R-kidney-12-Month_TCRB

description: Library name: 02R-kidney-12-Month_TCRB

value: Kidney

value: 12 Month


title: hypoxia, BGN siRNA-rep2

first: Miao

middle: miao

address: Kongjiang Road

institute: liumiaobiotech

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

source_name: cell

growth_protocol: HRMVPC cells were maintained in DMEM supplemented with 10% fetal bovine serun(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

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

value: cell

value: HRMVP(human retinal microvascular pericyte)

value: pericyte

value: BGN knockdown

value: hypoxia (1%O2) for 24h


title: 21ST_12

tag: batch


title: 21ST_11


title: 02R-kidney-3-Month_TCRB

description: Library name: 02R-kidney-3-Month_TCRB

value: 3 Month


title: hypoxia, BGN siRNA-rep1

tag: treatment


title: 02R-CD8-DRTCs

description: Library name: 02R-CD8-DRTCs

value: DRTC


title: 21ST_10

value: brain


title: 02R-CD4-DRTCs

description: Library name: 02R-CD4-DRTCs


title: 21ST_9


title: hypoxia, control siRNA-rep2

value: WT


title: R01-EV-Urine_Pellet-3M_TCRB

description: Library name: R01-EV-Urine_Pellet-3M_TCRB

value: Urine Pellet

value: Borderline


title: hypoxia, control siRNA-rep1


title: R01-EV-Urine_Pellet-12M_TCRB

description: Library name: R01-EV-Urine_Pellet-12M_TCRB


title: 02R-PBMC-12-Month_TCRB

description: Library name: 02R-PBMC-12-Month_TCRB

value: PBMC


title: R01-EV-PBMC-12M_TCRB

description: Library name: R01-EV-PBMC-12M_TCRB

value: Campath


title: R01-EV-Urine_Pellet-2W_TCRB

description: Library name: R01-EV-Urine_Pellet-2W_TCRB

value: 2 Week


title: 21ST_7

value: astrocyte


title: R01-EV-PBMC-3M_TCRB

description: Library name: R01-EV-PBMC-3M_TCRB


title: R01-EV-PBMC-PreTx_TCRB

description: Library name: R01-EV-PBMC-PreTx_TCRB

value: PreTx


title: R01-EV-Kidney-3M_TCRB

description: Library name: R01-EV-Kidney-3M_TCRB

value: Kidney


title: ITE treated, Male HUVECs, Rep.04

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes RSEM values for each Sample .

source_name: HUVECs

extract_protocol:
Total RNA samples were isolated from rat placentas using an RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and quality of each RNA sample were assessed using NanoDrop™ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100-bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA samples with high RNA integrity number (>8.5) were utilized in this study.
RNA libraries (one library per cell preparation) are generated using the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA) following the manufacturer’s instruction. In brief, 300ng total RNA of each sample is fragmented using divalent cations under elevated temperature, and purified. Double-stranded complementary DNAs (cDNAs) are synthesized using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. The cDNAs are ligated to Illumina adapters and amplified in a Linker Mediated PCR reaction (LM-PCR) for 9 cycles using PhusionTM DNA Polymerase and Illumina's PE genomic DNA primer set followed by purification (Agencourt AMPure XP beads, Qiagen).

tag: Sex

value: Male

value: Primary HUVECs

value: ITE


title: R01-EV-CD8-DRTC_TCRB

description: Library name: R01-EV-CD8-DRTC_TCRB


title: 21ST_5


title: ITE treated, Male HUVECs, Rep.02


title: 01R-Urine-pellet-12-Month_TCRB

description: Library name: 01R-Urine-pellet-12-Month_TCRB

value: 12 Month

value: Stable

value: campath


title: 21ST_4


title: 01R-Urine-pellet-6-Month_TCRB

description: Library name: 01R-Urine-pellet-6-Month_TCRB

value: 6 Month


title: 02R-kidney-PreTx_TCRB

description: Library name: 02R-kidney-PreTx_TCRB


title: 01R-Urine-pellet-3-Month_TCRB

description: Library name: 01R-Urine-pellet-3-Month_TCRB

value: 3 Month


title: 01R-PBMC-06-Month_TCRB

description: Library name: 01R-PBMC-06-Month_TCRB


title: 01R-PBMC-12-Month_TCRB

description: Library name: 01R-PBMC-12-Month_TCRB


title: 21ST_3

value: brain


title: 01R-PBMC-00PreTx_TCRB

description: Library name: 01R-PBMC-00PreTx_TCRB


title: 21ST_2


title: ITE treated, Male HUVECs, Rep.05


title: 21ST_1


title: 21ST_8


title: ITE treated, Female HUVECs, Rep.04

value: Female


title: 21ST_6


title: 01R-kidney-3-Month_TCRB

description: Library name: 01R-kidney-3-Month_TCRB


title: R01-EV-CD4-DRTC_TCRB

description: Library name: R01-EV-CD4-DRTC_TCRB

value: DRTC

value: Borderline


title: ITE treated, Male HUVECs, Rep.03


title: 01R-CD8-DRTCs

description: Library name: 01R-CD8-DRTCs


title: 01R-kidney-PreTx_TCRB

description: Library name: 01R-kidney-PreTx_TCRB


title: 21S2_12


title: 01R-CD4-DRTCs

description: Library name: 01R-CD4-DRTCs


title: WT 6

city: London

first: Alistair

last: Green

address: Imperial College London

country: United Kingdom

institute: Imperial College London

description:
Library name: AGD21
Column name in collapsedData.csv: AGD21

data_processing:
Reads were mapped using STARsolo (version 2.7.5c) to hg38.
Assembly: hg38
Supplementary files format and content: tab separated count files; DeSeq2

growth_protocol: DMEM 10% FBS

extract_protocol:
rna easy
TruSeq Stranded Total RNA with RiboZero

treatment_protocol: NO TREATMENT

value: WT


title: ITE treated, Female HUVECs, Rep.02


title: WT 5

description:
Library name: AGD20
Column name in collapsedData.csv: AGD20


title: 21S2_13


title: ITE treated, Male HUVECs, Rep.01


title: WT 4

description:
Library name: AGD19
Column name in collapsedData.csv: AGD19


title: ITE treated, Female HUVECs, Rep.01


title: ITE treated, Female HUVECs, Rep.05


title: ITE treated, Female HUVECs, Rep.03


title: WT 2

description:
Library name: AGD17
Column name in collapsedData.csv: AGD17


title: ITE treated, Female HUVECs, Rep.06


title: LHON_3460 cybrid 3

description:
Library name: AGD15
Column name in collapsedData.csv: AGD15


title: WT 1

description:
Library name: AGD16
Column name in collapsedData.csv: AGD16


title: 21S2_8


title: 21S2_10


title: LHON_3460 cybrid 2

description:
Library name: AGD14
Column name in collapsedData.csv: AGD14


title: Control, Male HUVECs, Rep.05

value: DMSO


title: Control, Male HUVECs, Rep.04


title: LHON_3460 cybrid 1

description:
Library name: AGD13
Column name in collapsedData.csv: AGD13


title: Control, Male HUVECs, Rep.03


title: 21S2_7

value: astrocyte


title: LHON_11778 cybrid 3

description:
Library name: AGD12
Column name in collapsedData.csv: AGD12


title: LHON_11778 cybrid 2

description:
Library name: AGD11
Column name in collapsedData.csv: AGD11


title: LHON_11778 cybrid 1

description:
Library name: AGD10
Column name in collapsedData.csv: AGD10


title: WT 3

description:
Library name: AGD18
Column name in collapsedData.csv: AGD18


title: Control, Male HUVECs, Rep.02


title: 21S2_6


title: 21S2_5


title: 21S2_11


title: BLaER1_ChIPseq_CT1_96h_Rep1

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
MNET-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using STAR aligner(Dobin et al., 2013) which reported a consistent 95% or more uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Reads were trimmed to the last 3’ base to identify the polymerase positions and the results were saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the analysis. DESeq2(Love et al., 2014) size factors were calculated from the counts and used for normalization. From the mNET-seq data we also calculated and corrected for antisense bias and cross contamination as described previously(Schwalb et al., 2016, Caizzi et al., 2021).
ChIPnexus-seq : ChIP-nexus data was processed as described in (He et al., 2015) with slight changes as follows. Reads were checked for adapter content using CutAdapt(version 2.3, Martin et al., ) and any regions with adapter were removed. Further to remove the region with barcodes, 9 bases from the 5’ end of the reads were trimmed. Reads were then mapped to a combined human and drosophila genome and samples reported a 74 percent uniquely mapped reads on average consistent with those from the original ChIP-nexus experiment(reference). Further processing was done as described in the pipeline (He et al., 2015). Duplicates were removed based on mapping locations and mapped reads were further trimmed to their 3’ end to extract the position of Pol II and saved as RLE lists for further analysis. Spike-ins were used for normalization.
ChIP-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using Bowtie2 aligner(Langmead et al., 2012) which reported a consistent 95% uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Duplicate reads were defined as those with the same start and end of mapping positions and were discarded from the data. Reads with an insert size of more than 500 bases were also discarded and the remaining reads which mapped uniquely were converted to and saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the factor that was immunoprecipitated. DESeq2(Love et al., 2014) size factors were calculated from the counts at the regions of interest and used for normalization.
Assembly: GRCh38
Supplementary files format and content: bigwig files

growth_protocol: BLaER1 cells were cultured in the growth media consisted of RPMI 1640 (Thermo Fisher Scientific, 31870-074) supplemented with 10% FBS (Thermo Fisher Scientific, 10500-064), 4 mM GlutaMAX (Thermo Fisher Scientific, 35050087), 25 mM HEPES (Thermo Fisher Scientific, 15630080) and 100 U/mL Penicillin-Streptomycin (Thermo Fisher Scientific, 15140122) at 37°C and 5% CO2. Biological replicates were cultured independently. BLaER1 cells were regularly examined and tested negative for the mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, rep-pt1).

extract_protocol:
ChIP-seq: ChIP-seq protocol was performed as described (Caizzi et al., 2021) with minor modifications listed below. Two biological replicates of 3e7 BLaER1 cells were collected at 0, 12, 24 h after transdifferentiation induction. For single crosslinking (Pol II, NELF-E ChIP-seq), cells were fixed in the growth media with 1% methanol-free formaldehyde (Thermo Fisher Scientific, 28908) at room temperature for 10 min. For double crosslinking (CDK9, Cyclin T1, INT11 ChIP-seq), cells were washed once with DPBS (Thermo Fisher Scientific, 14190169) and fixed in DPBS first with 2 mM DSG (Thermo Fisher Scientific, 20593) at room temperature for 20 min, then with 1% methanol-free formaldehyde (Thermo Fisher Scientific, 28908) at room temperature for 10 min. For quenching, 125 mM glycine (Sigma-Aldrich, 50046) was added to the cells and incubated at room temperature for 5 min. Fixed cells were spun down and washed twice with ice-cold DPBS (Thermo Fisher Scientific, 14190169). All the buffers were supplemented with protease inhibitor cocktail (Sigma-Aldrich, P8340) and phosphatase inhibitors (Millipore Sigma, 4906837001). Cell pellet was resuspended in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) and incubated on ice for 10 min. Isolated nuclei were washed once with ice-cold DPBS (Thermo Fisher Scientific, 14190169) and resuspended in sonication buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.4% SDS) followed by incubation on ice for 10 min. Suspension was transferred into 1 ml AFA milliTUBE (Covaris, 520130) and subjected to sonication using S220 Focused-ultrasonicator (Covaris) with the following parameters: 5% duty cycle, 140 W peak incident power, 200 cycles per burst, 960 sec processing time, 4-7°C bath temperature, continuous degassing mode, 8 water level. Sonicated chromatin was centrifuged at 4°C and 10,000 g for 15 min and supernatant was transferred to a new tube. DNA was quantified and analyzed on 1% agarose gel to confirm 200-500 bp fragment size distribution. Antibodies were coupled to Dynabeads Protein G (Thermo Fisher Scientific, 10004D) according to the manufacturer’s instructions. The following antibodies were used: RNA Polymerase II NTD antibody (Cell Signaling, 14958), Cyclin T1 antibody (Cell Signaling, 81464), CDK9 antibody (Abcam, ab239364), NELF-E antibody (Bethyl Laboratories, A301-913A), INT11 antibody (Bethyl Laboratories, A301-274A), Drosophila H2Av antibody (Active Motif, 61686). IP was performed with 50-100 µg chromatin per sample. Drosophila S2 spike-in chromatin was produced as described (Caizzi et al., 2021) and added in the amount of 122-400 ng per sample. 1% of each sample was kept as input and stored at 4°C. Chromatin was diluted with IP buffer (56.25 mM Tris-HCl pH 7.5, 157.5 mM NaCl, 1 mM EDTA, 1.125% Triton X-100, 0.1125% sodium deoxycholate) to obtain 0.1-0.05% SDS concentration. Chromatin was mixed with antibody-bead complexes and incubated on a rotating wheel at 4°C overnight. Next day, beads were washed five times with LiCl wash buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one time with TE buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA). DNA was eluted from the beads at 70°C for 10 min and decrosslinked at 65°C overnight along with input samples. DNA was subsequently treated with RNase A (Thermo Fisher Scientific, EN0531) and proteinase K (Thermo Fisher Scientific, AM2546) followed by precipitation in 100% EtOH.
ChIP-seq: Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instructions.

treatment_protocol: To induce the transdifferentiation, BLaER1 cells were brought to a density of 0.4e6 cells/mL and mixed with 100 nM β-Estradiol (Sigma-Aldrich, E2758-250MG), 10 ng/mL recombinant human IL-3 (PeproTech, 200-03) and 10 ng/mL recombinant human M-CSF (PeproTech, 300-25) in the growth media. For the 0 h control, BLaER1 cells were treated with the same concentration of solvents (ethanol and water). Cells were harvested at different time points: 0, 12, 24, 72, 96 h after induction for RNA extraction; 0, 12, 24, 72, 96 h after induction for mNET-seq; 0, 24, 96 h after induction for ChIP-seq; 0, 96 h after induction for ChIP-nexus. To inhibit transcription initiation, BLaER1 cells were collected at 0 or 96 h of transdifferentiation, brought to a density of 1e6 cells/mL and treated with 5 mM triptolide (TRP) (Sigma-Aldrich, T3652) or DMSO (Sigma-Aldrich, D2438) as a solvent control.

value: Human B-cell precursor leukemia

value: RCH-ACV stably expressing C/EBPaER-GFP

value: 96 h 100 nM beta-estradiol

tag: immunoprecipitation antibody


title: BLaER1_ChIPseq_CT1_96h_Rep2

value: Cyclin T1 antibody (Cell Signaling, 81464)


title: Control, Male HUVECs, Rep.01

value: Male

value: Primary HUVECs


title: 21S2_4


title: BLaER1_ChIPseq_CT1_24h_Rep1

value: 24 h 100 nM beta-estradiol


title: 21S2_3


title: BLaER1_ChIPseq_CT1_24h_Rep2


title: Control, Female HUVECs, Rep.06


title: BLaER1_ChIPseq_CT1_0h_Rep1


title: BLaER1_ChIPseq_CT1_0h_Rep2


title: Control, Female HUVECs, Rep.05


title: BLaER1_ChIPseq_CDK9_96h_Rep2

value: CDK9 antibody (Abcam, ab239364)


title: BLaER1_ChIPseq_CDK9_24h_Rep1


title: Control, Female HUVECs, Rep.04


title: 21S2_2


title: BLaER1_ChIPseq_CDK9_24h_Rep2


title: BLaER1_ChIPseq_CDK9_96h_Rep1


title: 21S2_1


title: Control, Female HUVECs, Rep.03


title: BLaER1_ChIPseq_Input_CT1_CDK9_96h_Rep1


title: Control, Female HUVECs, Rep.02


title: 21S_11


title: BLaER1_ChIPseq_CDK9_0h_Rep2


title: BLaER1_ChIPseq_CDK9_0h_Rep1


title: BLaER1_ChIPseq_Input_CT1_CDK9_24h_Rep1


title: BLaER1_ChIPseq_Input_CT1_CDK9_24h_Rep2


title: BLaER1_ChIPseq_Input_CT1_CDK9_0h_Rep1


title: 21S_9


title: 21S_7


title: BLaER1_ChIPseq_Input_CT1_CDK9_0h_Rep2


title: BLaER1_ChIPseq_Input_CT1_CDK9_96h_Rep2


title: 21S_5


title: BLaER1_ChIPNexusseq_PolII_TRP_6_96h_Rep2

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
MNET-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using STAR aligner(Dobin et al., 2013) which reported a consistent 95% or more uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Reads were trimmed to the last 3’ base to identify the polymerase positions and the results were saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the analysis. DESeq2(Love et al., 2014) size factors were calculated from the counts and used for normalization. From the mNET-seq data we also calculated and corrected for antisense bias and cross contamination as described previously(Schwalb et al., 2016, Caizzi et al., 2021).
ChIPnexus-seq : ChIP-nexus data was processed as described in (He et al., 2015) with slight changes as follows. Reads were checked for adapter content using CutAdapt(version 2.3, Martin et al., ) and any regions with adapter were removed. Further to remove the region with barcodes, 9 bases from the 5’ end of the reads were trimmed. Reads were then mapped to a combined human and drosophila genome and samples reported a 74 percent uniquely mapped reads on average consistent with those from the original ChIP-nexus experiment(reference). Further processing was done as described in the pipeline (He et al., 2015). Duplicates were removed based on mapping locations and mapped reads were further trimmed to their 3’ end to extract the position of Pol II and saved as RLE lists for further analysis. Spike-ins were used for normalization.
ChIP-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using Bowtie2 aligner(Langmead et al., 2012) which reported a consistent 95% uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Duplicate reads were defined as those with the same start and end of mapping positions and were discarded from the data. Reads with an insert size of more than 500 bases were also discarded and the remaining reads which mapped uniquely were converted to and saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the factor that was immunoprecipitated. DESeq2(Love et al., 2014) size factors were calculated from the counts at the regions of interest and used for normalization.
Assembly: GRCh38
Supplementary files format and content: bigwig files
Library strategy: ChIP-nexus

extract_protocol:
ChIP-nexus: Two biological replicates of BLaER1 cells were collected at 0 and 96 h post transdifferentiation induction and treated with 5 µM triptolide (Sigma-Aldrich, T3652) or DMSO (Sigma-Aldrich, D2438) as described in Treatments section. 3e7 cells per condition were single-crosslinked as described in ChIP-seq section. Cell lysis, nuclei isolation, chromatin shearing and quantification, IP were performed as described in ChIP-seq section. For IP, the following antibodies were used: RNA Polymerase II NTD antibody (Cell Signaling, 14958), Drosophila H2Av antibody (Active Motif, 61686). After IP, all downstream steps were performed exactly as in published protocol (Krueger et al., 2019).
ChIP-nexus: Libraries were prepared as described (Krueger et al., 2019) with minor modifications listed below. Amplified DNA libraries were size-selected using 4% E-Gel High-ReSolution Agarose Gels (Thermo Fisher Scientific, G501804) and purified using QIAquick Gel Extraction Kit (Qiagen, 28706X4) according to the manufacturer’s instructions.

value: 96 h 100 nM beta-estradiol; 6 min TRP

value: Pol II NTD antibody (Cell Signaling, 14958)


title: BLaER1_ChIPNexusseq_PolII_TRP_6_0h_Rep2

value: 6 min TRP


title: 21S_4

value: brain


title: BLaER1_ChIPNexusseq_PolII_TRP_6_0h_Rep1


title: BLaER1_ChIPNexusseq_PolII_TRP_6_96h_Rep1


title: BLaER1_ChIPNexusseq_PolII_TRP_30_96h_Rep2

value: 96 h 100 nM beta-estradiol; 30 min TRP


title: BLaER1_ChIPNexusseq_PolII_TRP_30_96h_Rep1


title: BLaER1_ChIPNexusseq_PolII_TRP_30_0h_Rep2

value: 30 min TRP


title: 21S_2


title: 21S_1


title: Control, Female HUVECs, Rep.01

value: Female


title: 21S_10


title: BLaER1_ChIPNexusseq_PolII_TRP_30_0h_Rep1


title: CTRL_7S16

value: in-slice control


title: BLaER1_ChIPNexusseq_PolII_DMSO_6_96h_Rep2

value: 96 h 100 nM beta-estradiol; 6 min DMSO


title: Brain, KOTsc, rep6

first: Richard

middle: L

last: Proia

state: MD

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

description:
KOTSC6
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt

data_processing:
Raw reads in FASTQ format were first processed to remove adapters, reads containing poly-N, and low-quality reads using fastp.
high-quality clean reads were mapped to reference genome mm10 (GRCm38) using hisat2 2.0.5.
Gene-expression quantification was performed using featureCounts 1.5.0-p3  and differential analysis performed using DESeq2 1.20.0
Pathway enrichment Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed using clusterProfiler 3.8.1 with corrected p-value set to <0.05 for significant enrichment.
Gene Set Enrichment Analysis (GSEQ) was performed using the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp
Assembly: mm10
Supplementary files format and content: RPKM values and gene count in tab-delimited text files

source_name: Brain

growth_protocol: Mice were housed under standard conditions with ad libitum access to water and food and with a 12 h dark/12 h light cycle.

extract_protocol:
Total RNA from one brain hemisphere each was isolated using miRNeasy Mini Kit(Qiagen).
3 ug of total RNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA with PolyA Selection Kit (New England Biolab).

value: Brain

value: No Treatment


title: HoxA9AA/Meis1, biological rep2

type: RNA

city: Boston

first: Daniel

middle: G.

last: Tenen

state: Massachusetts

address: 3 blackfan st

department: Harvard Medical School Initiative for RNA Medicine

institute: Harvard Medical School

description: Gene expression data from HoxA9AA/Meis1 mouse at disease onset

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Mouse Gene 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all of these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, Affymetrix)

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, Affymetrix)

data_processing: The Mouse Gene 1.0 ST arrays were processed using the ‘oligo’ Bioconductor package, quality-controlled with arrayQualityMetrics, and RMA normalized.

label: Biotin

source_name: BMCs from HoxA9AA/Meis1 mouse

label_protocol: Total RNA was prepared for hybridization with the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix

extract_protocol: Total RNA was extracted with TriReagent (Sigma-Aldrich, St. Louis, MO) and purified with RNeasy Micro Plus columns in conjunction with gDNA Eliminator columns (Qiagen, Hilden Germany) to remove residual genomic DNA.

value: Bone marrow


title: BLaER1_ChIPNexusseq_PolII_DMSO_6_96h_Rep1

value: Human B-cell precursor leukemia

value: RCH-ACV stably expressing C/EBPaER-GFP


title: CTRL_7ST2.12


title: BLaER1_ChIPNexusseq_PolII_DMSO_30_96h_Rep2

value: 96 h 100 nM beta-estradiol; 30 min DMSO


title: HoxA9AA/Meis1, biological rep3


title: BLaER1_ChIPNexusseq_PolII_DMSO_6_0h_Rep2

value: 6 min DMSO


title: CTRL_7ST10


title: CTRL_7ST11


title: Brain, KOTsc, rep4

description:
KOTSC4
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt


title: BLaER1_ChIPNexusseq_PolII_DMSO_30_96h_Rep1


title: BLaER1_ChIPNexusseq_PolII_DMSO_30_0h_Rep2

value: 30 min DMSO


title: HoxA9wt/Meis1, biological rep3

description: Gene expression data from HoxA9/Meis1 mouse at disease onset

source_name: BMCs from HoxA9/Meis1 mouse


title: BLaER1_ChIPNexusseq_PolII_DMSO_30_0h_Rep1


title: BLaER1_mNETseq_PolII_96h_Rep2

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
MNET-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using STAR aligner(Dobin et al., 2013) which reported a consistent 95% or more uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Reads were trimmed to the last 3’ base to identify the polymerase positions and the results were saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the analysis. DESeq2(Love et al., 2014) size factors were calculated from the counts and used for normalization. From the mNET-seq data we also calculated and corrected for antisense bias and cross contamination as described previously(Schwalb et al., 2016, Caizzi et al., 2021).
ChIPnexus-seq : ChIP-nexus data was processed as described in (He et al., 2015) with slight changes as follows. Reads were checked for adapter content using CutAdapt(version 2.3, Martin et al., ) and any regions with adapter were removed. Further to remove the region with barcodes, 9 bases from the 5’ end of the reads were trimmed. Reads were then mapped to a combined human and drosophila genome and samples reported a 74 percent uniquely mapped reads on average consistent with those from the original ChIP-nexus experiment(reference). Further processing was done as described in the pipeline (He et al., 2015). Duplicates were removed based on mapping locations and mapped reads were further trimmed to their 3’ end to extract the position of Pol II and saved as RLE lists for further analysis. Spike-ins were used for normalization.
ChIP-seq : Paired end reads of 75 bases length were collected for the samples. Reads were quality checked using FastQC(Andrews, S., 2010). Reads were mapped to the human genome(GRCh38) using Bowtie2 aligner(Langmead et al., 2012) which reported a consistent 95% uniquely mapped reads on an average for all samples. Further data processing was performed in R/Bioconductor environment using custom scripts. Duplicate reads were defined as those with the same start and end of mapping positions and were discarded from the data. Reads with an insert size of more than 500 bases were also discarded and the remaining reads which mapped uniquely were converted to and saved as RLE lists. Counts were calculated for the annotated transcripts using a custom R script for regions of interest depending on the factor that was immunoprecipitated. DESeq2(Love et al., 2014) size factors were calculated from the counts at the regions of interest and used for normalization.
Assembly: GRCh38
Supplementary files format and content: bigwig files
Library strategy: mNET-seq

extract_protocol:
mNET-seq: mNET-seq protocol was performed as described (Nojima et al., 2015; 2016) with minor modifications listed below. In short, two independent biological replicates of BLaER1 cells were subjected to transdifferentiation and collected at 0, 12, 24, 72, 96 h post induction. Cells were further used in the amount of 2e8 per replicate per time point. All the buffers were supplemented with protease inhibitor cocktail (Sigma-Aldrich, P8340) and phosphatase inhibitors (Millipore Sigma, 4906837001). After washing with DPBS (Thermo Fisher Scientific, 14190169), cellular fractionation of 2e7 cells per reaction was performed according to the previously published protocol (Conrad et al., 2017). Isolated chromatin was subjected to the Micrococcal Nuclease (MNase; NEB, M0247S) digestion at 37°C and 1,400 rpm for 90 sec followed by stopping the reaction with 25 mM EGTA (Bioworld, 40520008-1). The solution was clarified by centrifugation at 4°C and 13,000 g for 5 min and the supernatants corresponding to the same sample were pooled and utilized for immunoprecipitation (IP). Supernatant was diluted eightfold with IP buffer (50 mM Tris HCl pH 7.4, 150 mM NaCl, 0.05% NP-40, 0.3% empigen BB (Sigma-Aldrich, 30326)). RNA Polymerase II antibody (MBL Life science, MABI0601) was coupled to Dynabeads M-280 Sheep Anti-Mouse IgG (Thermo Fisher Scientific, 11201D) according to the manufacturer’s instructions and added to the digested chromatin at 30 µg per 2e8 cells. IP was performed at 4°C and 8 rpm on a rotating wheel for 1 h. Afterwards, beads were washed seven times with IP buffer and one time with PNKT buffer (1x T4 PNK buffer (NEB, M0236L), 0.1% Tween-20). For 5’ RNA phosphorylation, beads were resuspended in PNK reaction mix (T4 PNK buffer (NEB, M0236L), 0.1% Tween-20, 1 mM ATP (Cell Signaling Technology, 9804S), T4 Polynucleotide Kinase (phosphatase minus) (NEB, M0236L) and incubated at 37°C and 800 rpm for 10 min. After the reaction, beads were washed one time with IP buffer and mixed with QIAzol Lysis Reagent (Qiagen, 79306) by vortexing for 1 min. RNA was extracted according to the manufacturer’s instructions (Qiagen). Precipitation of RNA was performed with GlycoBlue Coprecipitant (Thermo Fisher Scientific, AM9515) in 100% ethanol overnight. RNA was size-selected in a range of 25-110 nt using a denaturing 6% polyacrylamide gel with 7M urea. Then, RNA was extracted from the gel in elution buffer (1 M NaOAc pH 5.5, 1 mM of EDTA pH 8.0) on a rotating wheel and precipitated with GlycoBlue Coprecipitant (Thermo Fisher Scientific, AM9515) in 100% ethanol overnight.
mNET-seq: Libraries were prepared with NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S) according to the manufacturer’s instructions. Libraries were size-selected with 4% E-Gel High-ReSolution Agarose Gels (Thermo Fisher Scientific, G501804) and purified using QIAquick Gel Extraction Kit (Qiagen, 28706X4) according to the manufacturer’s instructions.

value: 96 h 100 nM beta-estradiol

value: Pol II CTD antibody (MBL Life science, MABI0601)


title: Brain, KOTsc, rep3

description:
KOTSC3
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt


title: 7S2.14

data_processing:
Sequencing reads were mapped to the GRCm38.101 reference genome using STAR software version 2.6.0a.
TPM expression values based on ENSEMBL annotation version GRCm38.92 were calculated with RSEM (1.3.0).
Assembly: mm10
Supplementary files format and content: txt file

extract_protocol:
Single cells were sucked with an electrophysiological tip and transfer to tube for subsequent analysis.
SmartSeq2 + illumina protocols

value: Astrocyte


title: HoxA9wt/Meis1, biological rep2


title: BLaER1_mNETseq_PolII_96h_Rep1


title: Brain, KOTsc, rep2

description:
KOTSC2
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt


title: HoxA9AA/Meis1, biological rep1


title: Brain, KOTsc, rep1

description:
KOTSC1
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt


title: BLaER1_mNETseq_PolII_24h_Rep2

value: 24 h 100 nM beta-estradiol


title: 7S2.10

value: brain


title: 7S2.9


title: BLaER1_mNETseq_PolII_12h_Rep1

value: 12 h 100 nM beta-estradiol


title: BLaER1_mNETseq_PolII_72h_Rep2

value: 72 h 100 nM beta-estradiol


title: 7S2.12


title: BLaER1_mNETseq_PolII_0h_Rep2


title: 7S2.7


title: Brain, HexbKO, rep4

description:
HEXBKO4
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt

value: Hexb-/-


title: Brain, HexbKO, rep5

description:
HEXBKO5
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt


title: BLaER1_mNETseq_PolII_0h_Rep1


title: 7S2.6


title: Brain, HexbKO, rep6

description:
HEXBKO6
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt


title: Brain, KOTsc, rep5

description:
KOTSC5
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
KOTscvsTsc_deg_all.txt
KOTscvsWT_deg_all.txt


title: BLaER1_mNETseq_PolII_24h_Rep1


title: BLaER1_mNETseq_PolII_72h_Rep1


title: Brain, HexbKO, rep3

description:
HEXBKO3
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt


title: BLaER1_ChIPNexusseq_PolII_DMSO_6_0h_Rep1

value: Pol II NTD antibody (Cell Signaling, 14958)


title: M2 macrophages, Lucicebtide 10 μM, rep#2

city: Tarrytown

first: Claudio

last: Scuoppo

state: NY

address: 500 White Plains Rd Fl 2

institute: Sapience Therapeutics

description:
Library name: M5_1213
Column name in raw_counts.txt M5_1213

data_processing:
Reads containing adapters, containing N>10% (N represents base that could not be determined) and low-quality (qscore of over 50% bases is <=5) were removed.
HISAT2 was used for alignment
Quantification was performed using  featureCounts v1.5.0-p3.
Assembly: hg38
Supplementary files format and content: tab file with raw counts for each sample

source_name: hPBMCs-derived macrophages

growth_protocol: hPBMCs M2-like cultures were derived from a normal donor and incubated in Promo Cell M2 media, untreated, or in the presence of Lucicebtide 10 μM. Cultures were recovered at day 10.

extract_protocol:
Both floating and adherent cultures were collected. RNA was extracted using Rneasy mini kit (Quiagen).
Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Cell were left untreated (control) or treated with 10 μM Lucicebtide.

value: hPBMCs-derived macrophages

value: primary M2 macrophages

value: macrophages

value: Lucicebtide 10 μM


title: M2 macrophages, Lucicebtide 10 μM, rep#3

description:
Library name: M6_1213
Column name in raw_counts.txt M6_1213


title: M2 macrophages, Lucicebtide 10 μM, rep#1

description:
Library name: M4_1213
Column name in raw_counts.txt M4_1213


title: BLaER1_mNETseq_PolII_12h_Rep2

value: Human B-cell precursor leukemia

value: RCH-ACV stably expressing C/EBPaER-GFP


title: 7S2.2


title: Brain, HexbKO, rep2

description:
HEXBKO2
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt

value: Brain

value: No Treatment


title: 7S2.3


title: M2 macrophages, Untreated, rep#1

description:
Library name: M1_1213
Column name in raw_counts.txt M1_1213

value: Untreated


title: M2 macrophages, Untreated, rep#2

description:
Library name: M2_1213
Column name in raw_counts.txt M2_1213


title: Brain, HexbKO, rep1

description:
HEXBKO1
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsHexBKO_deg_all.txt
HexBKOvsWT_deg_all.txt


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), RNA-seq replicate 2

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Raw reads were processed using the GenPipes RNA sequencing pipeline v3.1.4. First, Trimmomatic v0.36 was used for quality trimming of raw reads and removal of sequencing adapters and then reads were aligned to the mouse reference genome assembly GRCm38/mm10 using STAR v2.5.3a. Next, several functions from Picard v2.9.0 were employed including MergeSamFiles for merging read alignment files of each sample, SortSam for sorting files by coordinate and MarkDuplicates for identifying read duplicates. Then, we incorporated the featureCounts function from Subread v2.0.6 to obtain raw counts corresponding to genomic regions of LINE, SINE, and LTR elements, extracted from RepeatMasker using the UCSC table browser. Finally, we employed DESeq2 v1.18.1 with R v3.4.3 to generate normalized counts for each element, which were then averaged across replicates for each experimental condition.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files containing genome-wide RPKM values (forward and reverse strands) for each experimental condition replicate.
Supplementary files format and content: BED file containing normalized counts for LINE, SINE and LTR transposable elements generated using the DESeq2 software.

source_name: R1 mESCs

growth_protocol: Dnmt1tet/tet mESCs were maintained on gelatin-coated plates, free of mouse embryonic fibroblast feeder cells, in mESC culture medium in humidified atmosphere with 5% CO2 at 37 °C. Cell culture plates were coated with 0.1% solution of gelatin (Sigma-Aldrich, G1890) in DPBS 1X (Corning, 21-031-CV), then placed in the incubator for 30 minutes after which excess gelatin was removed. Culture medium for mESCs consisted of DMEM (Corning, 10-013-CV) supplemented with 15% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D), 1% penicillin-streptomycin 100X (Corning, 30-002-CI) and 103 units/mL of recombinant mouse LIF protein (Sigma-Aldrich, ESG1107), which was stored at 4 °C for up to 1 week. Culture medium was changed every day and cell confluency was maintained below 80%. Trypsin-EDTA 0.25% (Thermo Fisher, 25200056) was used for passaging cell cultures, typically every other day.

extract_protocol:
The AllPrep DNA/RNA Mini Kit (QIAGEN, 80204) was used for RNA extraction.
The TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Kit (Illumina, 20020596) was used for library preparation.

treatment_protocol: To inactivate Dnmt1, Dnmt1tet/tet mESCs were treated with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), a tetracycline derivative, which was added to the culture medium for 6 days. Then, doxycycline treatment was stopped, and cells were maintained for 21 days. Samples were collected prior to doxycycline treatment (Dnmt1 control, CTL), immediately following doxycycline treatment (Dnmt1 inactive, INV), and after the 21-day period of recovery from doxycycline treatment (Dnmt1 rescue, RES).

value: R1 mESCs

value: Embryonic stem cell

value: Doxycycline (2 μg/mL) for 6 days, then recovery for 21 days


title: 7S19

value: brain

value: Astrocyte


title: Brain, TSC, rep6

description:
TSC6
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt


title: 7S18


title: 7S14


title: M2 macrophages, Untreated, rep#3

description:
Library name: M3_1213
Column name in raw_counts.txt M3_1213


title: 7S10


title: DMM WT biol rep 4

city: Münster

first: Joanna

last: Sherwood

address: Domagkstrasse 3

institute: University Hospital Münster

description:
Library name: DMM WT biol rep 4
DMMWTM1725_S4

data_processing:
Demultiplexing of samples was performed using bcl2fastq conversion tool (v2.19.1.403).
To maintain a minimum read length of 25 bp post trimming of adapters, Cutadapt (v2.5) software was executed (very few reads being contaminated ~3%) along with trimming of Ns. Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method was performed using HISAT2 software (v2.1.0 with parameters --rna-strandness RF –dta) against mouse reference genome (vGRCm38).
To populate the abundance of transcripts based on the reference genome and transcriptome, StringTie (v2.0.3 with parameters -e -B -G referencetranscripts.gtf) was run to generate output as table format files.
These files were processed using the script ‘prepDE.py’ from StringTie software to collect the raw gene expression levels for downstream processing.
Assembly: GRCm38
Supplementary files format and content: Tab separated value file including raw counts for all samples

source_name: Knee articular cartilage

extract_protocol:
RNA was harvested from femoral head and tibial plateau cartilage, 2-3 mice pooled per sample, RNA extracted using Trizol. 300ng of total RNA per sample used for library construction.
Sequencing libraries coonstructed using the TruSeq Stranded Total RNA with RiboZero as per manufacturer’s recommendations (Illumina, San Diego, CA, USA)

treatment_protocol: 10 week old male C57BL/6J wild type and Trpc1-/- mice subjected to destabilisation of the medical meniscus (DMM) of the right knee joint. Mice euthanised 2 weeks following DMM.

value: Knee articular cartilage

value: Wild type

value: DMM 2 weeks


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), RNA-seq replicate 1

value: Doxycycline (2 μg/mL) for 6 days


title: DMM TRPC1ko biol rep 1

description:
Library name: DMM TRPC1ko biol rep 1
DMMTRPKOM1360_S5

value: Trpc1 knockout


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), RNA-seq replicate 2


title: DMM TRPC1ko biol rep 3

description:
Library name: DMM TRPC1ko biol rep 3
DMMTRPKOM1364_S7


title: 7S13

first: Giacomo

address: Groshaderner Strasse 9


title: 7S12


title: Brain, TSC, rep3

description:
TSC3
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt


title: Brain, TSC, rep5

description:
TSC5
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt


title: HoxA9wt/Meis1, biological rep1

description: Gene expression data from HoxA9/Meis1 mouse at disease onset

value: Bone marrow


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), RNA-seq replicate 2


title: DMM WT biol rep 2

description:
Library name: DMM WT biol rep 2
DMMWTM1372_S2


title: DMM TRPC1ko biol rep 2

description:
Library name: DMM TRPC1ko biol rep 2
DMMTRPKOM1363_S6


title: Brain, TSC, rep1

description:
TSC1
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt


title: QGP-1, control, 3, K9Ac

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: Library name: CTR-3_K9Ac-17

data_processing:
Reads were mapped to a composite hg38+dm6 genome using BWA
Peak calling was performed using MACS2
Assembly: hg38 + dm6
Supplementary files format and content: bed files containing peak calls

source_name: Pancreas

growth_protocol: QGP-1 cells were all grown in DMEM/F12 (Gibco, Jenks, OK) with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco) at 37°C with 5% CO2 atmosphere.

extract_protocol:
QGP-1 cells were trypsinized, crosslinked to 1% formaldehyde for 10 min, and quenched with 125 mM glycine for 5 min at room temperature. After washing with TBS, cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspension in 200 μL fresh MNase digestion buffer containing proteinase inhibitor cocktail (Sigma), the lysates were incubated with 2000 units of MNase (New England Biolabs, Ipswich, MA) per 4 x 10^6 cells at 37°C for 20 min with continuous mixing in a thermal mixer. After adding 200 μL of sonication buffer (100 mM Tris-HCl, pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 20 min (30 s on/30 s off) using Bioruptor Twin (UCD-400) (Diagenode, Denville, NJ) and centrifuged at 21,130 x g for 10 min. The supernatants were collected, and the chromatin amount was estimated by the Qubit assay (Invitrogen).
ChIP-Rx; The chromatin was then incubated with anti-H3K27ac antibody (Cell Signaling Technology, Danvers, MA) or in-house generated anti-H3K9ac antibody (EDL lot 1) on a rocker overnight. Protein G-magnetic beads (30 μL, Life Technologies) were added, and further incubated for 3 hrs. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Germantown, MD) after the treatment of RNase A and proteinase K. The libraries were prepared from about 5 - 10 ng ChIP and input DNA using the ThruPLEX DNA-seq kit (TaKaRa, San Jose, CA). ChIP enrichment was validated by performing real-time PCR in library DNAs. The following primers were used: H3K27ac-positive control locus: SMARCA4-TSS-F: 5’-TTGGCGAAGCTGCGATCGGG-3’, SMARCA4-TSS-R: 5’-AGGGGACCGCTAATGCCCGT-3’; ACTB-TSS-F: 5’-CCTCATGGCCTTGTCACAC-3’, ACTB-TSS-R: 5’-GCCCTTTCTCACTGGTTCTCT-3’; H3K27ac-negative control locus: Ch19-intergenic-F: 5’-AGCTTGTCTTTCCCAAGTTTACTC-3’, Ch19-intergenic-R: 5’-TAGCTGTCGCACTTCAGAGGA-3’.

treatment_protocol: Cells in the cointrol group were maintained in fresh DMEM/F12 medium, while those in butyrate group were maintained in fresh DMEM/F12 containing 5 mM butyrate for 24h.

value: Pancreas

value: human pancreatic islet cell carcinoma cell line

value: WT

value: medium

tag: chip antibody


title: Brain, TSC, rep2

description:
TSC2
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt

value: Brain

value: No Treatment


title: 7S9

last: Masserdotti

institute: Helmholtz Zentrum

source_name: brain


title: DMM WT biol rep 1

description:
Library name: DMM WT biol rep 1
DMMWTM1370_S1


title: Brain, WT Control, rep6

description:
WT6
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), RNA-seq replicate 1

tag: cell line

value: R1 mESCs


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), RNA-seq replicate 1

value: Embryonic stem cell

tag: genotype

value: Untreated


title: QGP-1, control, 3, K27Ac

description: Library name: CTR-3_K27Ac-18


title: sample12_cells.1111.to.1115

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were aligned using STAR and quantified using RSEM. Counts were then imported into R statistical computing environment for further processing.
Assembly: Mus musculus (GRCm38 mm10)
Supplementary files format and content: RDS file (SingleCellExperiment) containing all raw counts prior to exclusion of cells.
Supplementary files format and content: csv file with raw read counts

source_name: Utricle

extract_protocol:
Smart-seq2
Smart-seq2

value: Utricle

value: utricle cell


title: QGP-1, control, 3, Input

description: Library name: CTR-3_Input-24

value: Input


title: Brain, WT Control, rep5

description:
WT5
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt


title: sample11_cells.1001.to.1100


title: QGP-1, control, 2, K9Ac

description: Library name: CTR-2_K9Ac-14


title: 7S5

city: Planegg-Martinstied

value: brain

value: Astrocyte


title: DMM WT biol rep 3

description:
Library name: DMM WT biol rep 3
DMMWTM1726_S3

value: Knee articular cartilage

value: Wild type

value: DMM 2 weeks


title: 7S7


title: Brain, WT Control, rep4

description:
WT4
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt


title: sample10_cells.901.to.1000


title: Brain, WT Control, rep1

description:
WT1
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt


title: QGP-1, control, 2, K27Ac

description: Library name: CTR-2_K27Ac-15

value: Pancreas


title: 7S1


title: 7S4


title: sample7_cells.601.to.700


title: sample9_cells.801.to.900


title: QGP-1, control, 2, Input

description: Library name: CTR-2_Input-23

value: human pancreatic islet cell carcinoma cell line


title: 7S2


title: 7S8


title: 7ST2.13


title: 7ST2.19


title: QGP-1, control, 1, K27Ac

description: Library name: CTR-1_K27Ac-12

value: WT


title: Brain, TSC, rep4

description:
TSC4
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
KOTscvsTsc_deg_all.txt
WTvsTsc_deg_all.txt


title: sample6_cells.501.to.600


title: QGP-1, control, 1, Input

description: Library name: CTR-1_Input-22

value: medium


title: RNA from S. cerevisiae cells expressing GFP-tagged MeCP2 T158M E2 grown in  CSM-uracil and pulsed with 4-tU replicate 1

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

institute: University Of British Columbia

description: Library name: T158M_1_RNA

data_processing:
Bioinformatic analysis was performed as previously described (Ridenour and Donczew 2024). Reads were processed with fastp and bbduk to trim adapter sequences and polyA tails. The trim package was applied so that subsequent steps used read positions 14-56 for analysis. Reads were then analyzed with the slamdunk, alleyoop, and multiqc packages. A minimum of 2x T>C conversions was used as the threshold for T>C reads in slamdunk analysis, and a minimum base quality of 26 was used for T>C calls.
Assembly: saccer3.fa
Supplementary files format and content: Slamdunk counts

organism: Saccharomyces cerevisiae

extract_protocol:
RNA was extracted using hot acid phenol  and 10 µg of purified RNA was alkylated with fresh iodoacetamide.
RNA samples were subject to polyA capture, reverse transcription, and amplification according to the Illumina Stranded mRNA prep workflow.

treatment_protocol: Cells were treated with 4-thiouracil for eight minutes and flash frozen.

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E2_T158M

value: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for four hours.  Cells were then treated with 4-thiouracil for 8 minutes


title: RNA from S. cerevisiae cells expressing GFP-tagged MeCP2 T158M E2 grown in  CSM-uracil and pulsed with 4-tU replicate 2

description: Library name: T158M_2_RNA

growth_protocol: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for four hours.


title: Brain, WT Control, rep3

institute: National Institutes of Health

description:
WT3
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt

value: Brain

value: No Treatment


title: 7ST2.10


title: QGP-1, butyrate,3, K27Ac

description: Library name: Bub-3_K27Ac-9

value: 5 mM butyrate


title: RNA from S. cerevisiae cells expressing GFP-tagged MeCP2 E2 grown in CSM-uracil and pulsed with 4-tU replicate 2

description: Library name: WT_2_RNA

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E2


title: sample8_cells.701.to.800

value: Utricle

value: utricle cell


title: QGP-1, butyrate,3, K9Ac

description: Library name: Bub-3_K9Ac-8


title: 7ST2.11

value: brain


title: Brain, WT Control, rep2

description:
WT2
gene_fpkm.txt
gene_count.txt
gene_fpkm_group.txt
HexBKOvsWT_deg_all.txt
KOTscvsWT_deg_all.txt
WTvsTsc_deg_all.txt


title: sample4_cells.301.to.400


title: RNA from S. cerevisiae cells expressing GFP-tagged MeCP2 E2 grown in CSM-uracil and pulsed with 4-tU replicate 1

description: Library name: WT_1_RNA


title: QGP-1, control, 1, K9Ac

description: Library name: CTR-1_K9Ac-11


title: RNA from S. cerevisiae cells with vector alone grown in  CSM-uracil and pulsed with 4-tU replicate 2

description: Library name: vector_2_RNA

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pRS416


title: 7ST2.8

value: Astrocyte


title: 7ST2.9


title: QGP-1, butyrate, 3, Input

description: Library name: Bub-3_Input-21

value: Input


title: sample2_cells.101.to.200


title: sample1_cells.1.to.100


title: QGP-1, butyrate, 2, Input

description: Library name: Bub-2_Input-20


title: QGP-1, butyrate,2, K9Ac

description: Library name: Bub-2_K9Ac-5


title: sample5_cells.401.to.500


title: ChIP_GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

description:
T158M_2_ChIP
ChIP DNA from GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2

data_processing:
Sequence reads were trimmed for adapter sequences using cutadapt (http://cutadapt.readthedocs.io/en/stable/) and mapped to the Saccer3 genome build using BWA-MEM. Only reads mapped in proper pairs by BWA-MEM were used in subsequent analysis.
Data was converted to bigwig files of using  DeepTools in the Galaxy web platform. bamCoverage was used to analyze IP and input samples separately, while bamCompare was used to compare IP and input signal. Parameters used were: bin size = 5 bp, mapping quality threshold >= 25, paired-end read extension, duplicate reads removed. IP reads were first multiplied by a scaling factor (1000 / S. pombe IP reads). IP and input samples were normalized based on the relative number of reads mapping to the genome of the S. pombe spike-in. “IP/input” analyses are presented as the log2 of IP signal divided by input signal, in which IP reads were multiplied by a scaling factor (1000 / S. pombe IP reads). This value of 1000 was used an arbitrary scaling factor while dividing by S. pombe spike-in reads, similar to the use of scaling factors in previous work64. Input samples were multiplied by a scaling factor of (1 / S. pombe input reads).
Assembly: saccer3.fa
Supplementary files format and content: bigwig files of read count normalized to S. pombe spike-ins
Supplementary files format and content: log2 (ChIP/input) bigwig files normalized to S. pombe spike-ins

growth_protocol: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for one hour.

extract_protocol:
Cells (450 million S.cerevisiae and 68 million Schizosaccharomyces pombe as spike-in) were resuspended in 0.6 mL of lysis buffer (50 mM Hepes-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and lysed by bead beating before centrifugation, then resuspended in 1 mL. Samples were sonicated with a Covaris S220 focused-ultrasonicator (peak power 150 W for 7min with 30s cycling off/on, duty factor 14, 200 cycles/burst). One hundred microlitres of lysate was reserved as input and 750 uL was used for immunoprecipitation. Samples were precleared with protein G Dynabeads™ (ThermoFisher cat# 10003D) for 1 hour, incubated overnight anti-GFP antibody (Abcam cat# ab290), and incubated with protein G beads for 1 hour, all at 4°C. Beads were washed twice with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 0.5 mM EDTA, 1% triton X-100, 0.1% sodium deoxycholate), twice with lysis buffer with 500 mM NaCl, and twice with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.6% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), before 1 wash with TE (pH 8). Samples were eluted in elution buffer (TE pH 8, 1% sodium dodecyl sulfate, 150 mM NaCl, 5 mM dithiothreitol) three times by incubation at 65°C for ten minutes, with shaking.
DNA was end-repaired, A-tailed, and ligated to adapters before 17 cycles of PCR amplification with indexed primers. All DNA purification steps used Solid Phase Reversible Immobilization magnetic beads (Omega, M1378). Samples were pooled, gel-purified (200-600 bp fragments) and sequenced on an Illumina NextSeq.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 15 min, quenched with 300 mM glycine for 5 min, and frozen.

value: anti-GFP antibody (Abcam cat# ab290)

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E1_T158M


title: 7ST9


title: 7ST2.7


title: ChIP_GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
T158M_1_ChIP
ChIP DNA from GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1

value: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for one hour


title: sample3_cells.201.to.300


title: QGP-1, butyrate,2, K27Ac

description: Library name: Bub-2_K27Ac-6

value: Pancreas

value: human pancreatic islet cell carcinoma cell line

value: WT